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HEADER OXYGEN TRANSPORT 12-DEC-95 1FSL TITLE FERRIC SOYBEAN LEGHEMOGLOBIN COMPLEXED WITH NICOTINATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEGHEMOGLOBIN A; COMPND 3 CHAIN: A, B; COMPND 4 OTHER_DETAILS: FE(III), PH 6.0 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEAN; SOURCE 4 ORGAN: ROOT NODULE KEYWDS HEME, RESPIRATORY PROTEIN, NITROGEN FIXATION, MULTIGENE KEYWDS 2 FAMILY, OXYGEN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR P.J.ELLIS,J.M.GUSS,H.C.FREEMAN REVDAT 1 26-JUN-96 1FSL 0 JRNL AUTH P.J.ELLIS,C.A.APPLEBY,J.M.GUSS,W.N.HUNTER, JRNL AUTH 2 D.L.OLLIS,H.C.FREEMAN JRNL TITL STRUCTURE OF FERRIC SOYBEAN LEGHEMOGLOBIN A JRNL TITL 2 NICOTINATE AT 2.3 A RESOLUTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 53 302 1997 JRNL REFN ASTM ABCRE6 DK ISSN 0907-4449 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.L.OLLIS,C.A.APPLEBY,P.M.COLMAN,A.E.CUTTEN, REMARK 1 AUTH 2 J.M.GUSS,M.P.VENKATAPPA,H.C.FREEMAN REMARK 1 TITL CRYSTAL STRUCTURE OF SOYBEAN FERRIC LEGHAEMOGLOBIN REMARK 1 TITL 2 A NICOTINATE AT A RESOLUTION OF 3.3 ANGSTROM REMARK 1 REF AUST.J.CHEM. V. 36 451 1983 REMARK 1 REFN ASTM AJCHAS AT ISSN 0004-9425 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROFFT REMARK 3 AUTHORS : KONNERT,HENDRICKSON,FINZEL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 49.5 REMARK 3 NUMBER OF REFLECTIONS : 6877 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.158 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 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2168 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 172 REMARK 3 SOLVENT ATOMS : 70 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.30 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.009 ; 0.015 REMARK 3 ANGLE DISTANCE (A) : 0.016 ; 0.015 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.025 ; 0.030 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.010 ; 0.015 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.078 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.150 ; 0.250 REMARK 3 MULTIPLE TORSION (A) : 0.198 ; 0.250 REMARK 3 H-BOND (X...Y) (A) : 0.182 ; 0.250 REMARK 3 H-BOND (X-H...Y) (A) : 0.172 ; 0.250 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 2.200 ; 3.000 REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 0.590 ; 1.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.030 ; 1.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 0.520 ; 1.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 0.940 ; 1.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FSL 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 : 1981 REMARK 200 TEMPERATURE (KELVIN) : 295.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 6 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS CAD-4 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : BRUKER NONIUS FAST REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ENRAF-NONIUS REMARK 200 DATA SCALING SOFTWARE : PROTEIN (STEIGEMANN) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14153 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 1.300 REMARK 200 R MERGE (I) : 0.06100 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: MIR REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,1/2+Y,-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 28.27500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 2 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 BIOMOLECULE: 2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 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 LYS B 142 98.76 115.66 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 69 DISTANCE = 12.13 ANGSTROMS DBREF 1FSL A 1 143 UNP P02238 LGBA_SOYBN 1 143 DBREF 1FSL B 1 143 UNP P02238 LGBA_SOYBN 1 143 SEQRES 1 A 143 VAL ALA PHE THR GLU LYS GLN ASP ALA LEU VAL SER SER SEQRES 2 A 143 SER PHE GLU ALA PHE LYS ALA ASN ILE PRO GLN TYR SER SEQRES 3 A 143 VAL VAL PHE TYR THR SER ILE LEU GLU LYS ALA PRO ALA SEQRES 4 A 143 ALA LYS ASP LEU PHE SER PHE LEU ALA ASN GLY VAL ASP SEQRES 5 A 143 PRO THR ASN PRO LYS LEU THR GLY HIS ALA GLU LYS LEU SEQRES 6 A 143 PHE ALA LEU VAL ARG ASP SER ALA GLY GLN LEU LYS ALA SEQRES 7 A 143 SER GLY THR VAL VAL ALA ASP ALA ALA LEU GLY SER VAL SEQRES 8 A 143 HIS ALA GLN LYS ALA VAL THR ASP PRO GLN PHE VAL VAL SEQRES 9 A 143 VAL LYS GLU ALA LEU LEU LYS THR ILE LYS ALA ALA VAL SEQRES 10 A 143 GLY ASP LYS TRP SER ASP GLU LEU SER ARG ALA TRP GLU SEQRES 11 A 143 VAL ALA TYR ASP GLU LEU ALA ALA ALA ILE LYS LYS ALA SEQRES 1 B 143 VAL ALA PHE THR GLU LYS GLN ASP ALA LEU VAL SER SER SEQRES 2 B 143 SER PHE GLU ALA PHE LYS ALA ASN ILE PRO GLN TYR SER SEQRES 3 B 143 VAL VAL PHE TYR THR SER ILE LEU GLU LYS ALA PRO ALA SEQRES 4 B 143 ALA LYS ASP LEU PHE SER PHE LEU ALA ASN GLY VAL ASP SEQRES 5 B 143 PRO THR ASN PRO LYS LEU THR GLY HIS ALA GLU LYS LEU SEQRES 6 B 143 PHE ALA LEU VAL ARG ASP SER ALA GLY GLN LEU LYS ALA SEQRES 7 B 143 SER GLY THR VAL VAL ALA ASP ALA ALA LEU GLY SER VAL SEQRES 8 B 143 HIS ALA GLN LYS ALA VAL THR ASP PRO GLN PHE VAL VAL SEQRES 9 B 143 VAL LYS GLU ALA LEU LEU LYS THR ILE LYS ALA ALA VAL SEQRES 10 B 143 GLY ASP LYS TRP SER ASP GLU LEU SER ARG ALA TRP GLU SEQRES 11 B 143 VAL ALA TYR ASP GLU LEU ALA ALA ALA ILE LYS LYS ALA HET HEM A 144 73 HET NIO A 145 13 HET HEM B 144 73 HET NIO B 145 13 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NIO NICOTINIC ACID HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 NIO 2(C6 H5 N O2) FORMUL 7 HOH *70(H2 O) HELIX 1 A1 THR A 4 ALA A 20 1 17 HELIX 2 B1 ASN A 21 ALA A 37 1 17 HELIX 3 C1 PRO A 38 PHE A 44 5 7 HELIX 4 E1 ASN A 55 GLY A 80 1 26 HELIX 5 F1 ASP A 85 GLN A 94 1 10 HELIX 6 G1 THR A 98 VAL A 117 1 20 HELIX 7 H1 SER A 122 LYS A 141 1 20 HELIX 8 A2 THR B 4 ALA B 20 1 17 HELIX 9 B2 ASN B 21 ALA B 37 1 17 HELIX 10 C2 PRO B 38 PHE B 44 5 7 HELIX 11 E2 ASN B 55 GLY B 80 1 26 HELIX 12 F2 ASP B 85 GLN B 94 1 10 HELIX 13 G2 THR B 98 VAL B 117 1 20 HELIX 14 H2 SER B 122 LYS B 141 1 20 LINK FE HEM A 144 NE2 HIS A 92 LINK FE HEM A 144 N NIO A 145 LINK FE HEM B 144 NE2 HIS B 92 LINK FE HEM B 144 N NIO B 145 CRYST1 52.690 56.550 57.800 90.00 109.90 90.00 P 1 21 1 4 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 0.018979 0.000000 0.006870 0.00000 SCALE2 0.000000 0.017683 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018400 0.00000 MTRIX1 1 -0.461976 0.030242 0.886377 -41.53064 1 MTRIX2 1 -0.021546 -0.999506 0.022872 45.05125 1 MTRIX3 1 0.886631 -0.008532 0.462400 19.71374 1