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HEADER OXYGEN TRANSPORT 26-AUG-94 1HLM TITLE AMINO ACID SEQUENCE OF A GLOBIN FROM THE SEA CUCUMBER TITLE 2 CAUDINA (MOLPADIA) ARENICOLA COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN (CYANO MET); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAUDINA ARENICOLA KEYWDS OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.L.HACKERT,D.T.MITCHELL,S.R.ERNST REVDAT 1 07-FEB-95 1HLM 0 JRNL AUTH F.MAURI,J.OMNAAS,L.DAVIDSON,C.WHITFILL,G.B.KITTO JRNL TITL AMINO ACID SEQUENCE OF A GLOBIN FROM THE SEA JRNL TITL 2 CUCUMBER CAUDINA (MOLPADIA) ARENICOLA. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1078 63 1991 JRNL REFN ASTM BBACAQ NE ISSN 0006-3002 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.M.CARSON,T.R.BOWERS,G.B.KITTO,M.L.HACKERT REMARK 1 TITL PRELIMINARY CRYSTALLOGRAPHIC DATA ON MONOMERIC AND REMARK 1 TITL 2 DIMERIC HEMOGLOBINS FROM THE SEA CUCUMBER, REMARK 1 TITL 3 MOLPADIA ARENICOLA REMARK 1 REF J.BIOL.CHEM. V. 254 7400 1979 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH G.B.KITTO,D.ERWIN,R.WEST,J.OMNAAS REMARK 1 TITL N-TERMINAL SUBSTITUTION OF SOME SEA CUCUMBER REMARK 1 TITL 2 HEMOGLOBINS REMARK 1 REF COMP.BIOCHEM.PHYSIOL. B: V. 55 105 1976 REMARK 1 REF 2 COMP.BIOCHEM. REMARK 1 REFN ASTM CBPBB8 UK ISSN 0305-0491 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 5.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1247 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 5 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 3.51 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.93 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HLM COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-17) REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,1/2+Z REMARK 290 3555 1/2-Y,1/2+X,1/4+Z REMARK 290 4555 1/2+Y,1/2-X,3/4+Z REMARK 290 5555 1/2-X,1/2+Y,1/4-Z REMARK 290 6555 1/2+X,1/2-Y,3/4-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,1/2-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.75000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 38.50000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.37500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.50000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 38.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 46.12500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 38.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 15.37500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 38.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 38.50000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 46.12500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 30.75000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 C CYN 160 FE HEM 159 1.78 REMARK 500 NE2 HIS A 104 FE HEM 159 2.02 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 12 -79.80 69.59 REMARK 500 SER A 67 -149.72 175.21 REMARK 500 THR A 154 -110.94 27.34 DBREF 1HLM A 1 158 UNP P80017 GLBD_CAUAR 1 158 SEQRES 1 A 158 GLY ALA THR GLN SER PHE GLN SER VAL GLY ASP LEU THR SEQRES 2 A 158 PRO ALA GLU LYS ASP LEU ILE ARG SER THR TRP ASP GLN SEQRES 3 A 158 LEU MET THR HIS ARG THR GLY PHE VAL ALA ASP VAL PHE SEQRES 4 A 158 ILE ARG ILE PHE HIS ASN ASP PRO THR ALA GLN ARG LYS SEQRES 5 A 158 PHE PRO GLN MET ALA GLY LEU SER PRO ALA GLU LEU ARG SEQRES 6 A 158 THR SER ARG GLN MET HIS ALA HIS ALA ILE ARG VAL SER SEQRES 7 A 158 ALA LEU MET THR THR TYR ILE ASP GLU MET ASP THR GLU SEQRES 8 A 158 VAL LEU PRO GLU LEU LEU ALA THR LEU THR ARG THR HIS SEQRES 9 A 158 ASP LYS ASN HIS VAL GLY LYS LYS ASN TYR ASP LEU PHE SEQRES 10 A 158 GLY LYS VAL LEU MET GLU ALA ILE LYS ALA GLU LEU GLY SEQRES 11 A 158 VAL GLY PHE THR LYS GLN VAL HIS ASP ALA TRP ALA LYS SEQRES 12 A 158 THR PHE ALA ILE VAL GLN GLY VAL LEU ILE THR LYS HIS SEQRES 13 A 158 ALA SER HET CYN 160 2 HET ACE A 0 3 HET HEM 159 43 HETNAM CYN CYANIDE ION HETNAM ACE ACETYL GROUP HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 CYN C N 1- FORMUL 3 ACE C2 H4 O FORMUL 4 HEM C34 H32 FE N4 O4 FORMUL 5 HOH *5(H2 O) HELIX 1 A THR A 13 MET A 28 1 16 HELIX 2 B ARG A 31 ASN A 45 1 15 HELIX 3 C ASP A 46 ARG A 51 1 6 HELIX 4 E ARG A 68 ASP A 86 1DISTAL HIS 73 19 HELIX 5 F LEU A 93 ASN A 107 1PROXIMAL HIS 104 15 HELIX 6 G GLY A 110 GLU A 128 1 19 HELIX 7 H THR A 134 VAL A 148 1 15 TURN 1 B/C ASP A 46 ALA A 49 BETA BEND, I + 3 LINK C ACE A 0 N GLY A 1 SITE 1 HEM 2 HEM 159 CYN 160 CRYST1 77.000 77.000 61.500 90.00 90.00 90.00 P 41 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012987 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012987 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016260 0.00000