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HEADER OXIDOREDUCTASES(ACTING ON CH-NH2 DONOR) 11-JAN-95 1HTP TITLE REFINED STRUCTURES AT 2 ANGSTROMS AND 2.2 ANGSTROMS OF THE TITLE 2 TWO FORMS OF THE H-PROTEIN, A LIPOAMIDE-CONTAINING PROTEIN TITLE 3 OF THE GLYCINE DECARBOXYLASE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: H-PROTEIN; COMPND 3 CHAIN: A; COMPND 4 EC: 1.4.4.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PISUM SATIVUM KEYWDS OXIDOREDUCTASES(ACTING ON CH-NH2 DONOR) EXPDTA X-RAY DIFFRACTION AUTHOR S.PARES,C.COHEN-ADDAD REVDAT 2 01-APR-03 1HTP 1 JRNL REVDAT 1 31-MAR-95 1HTP 0 JRNL AUTH C.COHEN-ADDAD,S.PARES,L.SIEKER,M.NEUBURGER,R.DOUCE JRNL TITL THE LIPOAMIDE ARM IN THE GLYCINE DECARBOXYLASE JRNL TITL 2 COMPLEX IS NOT FREELY SWINGING. JRNL REF NAT.STRUCT.BIOL. V. 2 63 1995 JRNL REFN ASTM NSBIEW US ISSN 1072-8368 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.PARES,C.COHEN-ADDAD,L.SIEKER,M.NEUBURGER,R.DOUCE REMARK 1 TITL X-RAY STRUCTURE DETERMINATION AT 2.6 ANGSTROMS REMARK 1 TITL 2 RESOLUTION OF A LIPOATE-CONTAINING PROTEIN: THE REMARK 1 TITL 3 H-PROTEIN OF THE GLYCINE DECARBOXYLASE COMPLEX REMARK 1 TITL 4 FROM PEA LEAVES REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 91 4850 1994 REMARK 1 REFN ASTM PNASA6 US ISSN 0027-8424 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 5457 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) : 0.185 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 : 1180 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.50 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) : 0.20 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) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 2.90 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.10 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 1HTP 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 : 5684 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 (%) : 91.0 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 (%): 40.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 1/2-X,1/2+Y,-Z REMARK 290 4555 1/2+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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 30.67000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.69000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.67000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.69000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 14 DISTANCE = 8.11 ANGSTROMS REMARK 525 HOH 16 DISTANCE = 9.46 ANGSTROMS REMARK 525 HOH 17 DISTANCE = 9.04 ANGSTROMS REMARK 525 HOH 19 DISTANCE = 10.80 ANGSTROMS REMARK 525 HOH 20 DISTANCE = 11.26 ANGSTROMS REMARK 525 HOH 23 DISTANCE = 10.97 ANGSTROMS REMARK 525 HOH 24 DISTANCE = 8.57 ANGSTROMS REMARK 525 HOH 26 DISTANCE = 5.73 ANGSTROMS REMARK 525 HOH 67 DISTANCE = 8.84 ANGSTROMS REMARK 525 HOH 69 DISTANCE = 7.40 ANGSTROMS REMARK 525 HOH 70 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH 71 DISTANCE = 5.22 ANGSTROMS REMARK 525 HOH 72 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH 73 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH 88 DISTANCE = 5.06 ANGSTROMS REMARK 525 HOH 94 DISTANCE = 5.05 ANGSTROMS REMARK 525 HOH 96 DISTANCE = 5.66 ANGSTROMS REMARK 525 HOH 97 DISTANCE = 8.02 ANGSTROMS REMARK 525 HOH 102 DISTANCE = 5.52 ANGSTROMS REMARK 525 HOH 107 DISTANCE = 7.30 ANGSTROMS REMARK 525 HOH 108 DISTANCE = 5.16 ANGSTROMS REMARK 525 HOH 109 DISTANCE = 9.11 ANGSTROMS REMARK 525 HOH 110 DISTANCE = 9.34 ANGSTROMS REMARK 525 HOH 111 DISTANCE = 11.55 ANGSTROMS REMARK 525 HOH 112 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH 113 DISTANCE = 5.24 ANGSTROMS REMARK 525 HOH 115 DISTANCE = 5.19 ANGSTROMS REMARK 525 HOH 116 DISTANCE = 7.55 ANGSTROMS REMARK 525 HOH 117 DISTANCE = 8.81 ANGSTROMS REMARK 525 HOH 118 DISTANCE = 7.44 ANGSTROMS REMARK 525 HOH 124 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH 127 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH 131 DISTANCE = 9.10 ANGSTROMS DBREF 1HTP A 1 131 UNP P16048 GCSH_PEA 35 165 SEQRES 1 A 131 SER ASN VAL LEU ASP GLY LEU LYS TYR ALA PRO SER HIS SEQRES 2 A 131 GLU TRP VAL LYS HIS GLU GLY SER VAL ALA THR ILE GLY SEQRES 3 A 131 ILE THR ASP HIS ALA GLN ASP HIS LEU GLY GLU VAL VAL SEQRES 4 A 131 PHE VAL GLU LEU PRO GLU PRO GLY VAL SER VAL THR LYS SEQRES 5 A 131 GLY LYS GLY PHE GLY ALA VAL GLU SER VAL LYS ALA THR SEQRES 6 A 131 SER ASP VAL ASN SER PRO ILE SER GLY GLU VAL ILE GLU SEQRES 7 A 131 VAL ASN THR GLY LEU THR GLY LYS PRO GLY LEU ILE ASN SEQRES 8 A 131 SER SER PRO TYR GLU ASP GLY TRP MET ILE LYS ILE LYS SEQRES 9 A 131 PRO THR SER PRO ASP GLU LEU GLU SER LEU LEU GLY ALA SEQRES 10 A 131 LYS GLU TYR THR LYS PHE CYS GLU GLU GLU ASP ALA ALA SEQRES 11 A 131 HIS HET OSS 63 17 HETNAM OSS 6-(HYDROXYETHYLDITHIO)-8-(AMINOMETHYLTHIO)OCTANOIC HETNAM 2 OSS ACID FORMUL 2 OSS C11 H23 N O3 S3 FORMUL 3 HOH *145(H2 O) HELIX 1 1 ASP A 29 LEU A 35 1 7 HELIX 2 2 THR A 81 GLY A 85 5 5 HELIX 3 3 PRO A 87 SER A 92 5 6 HELIX 4 4 PRO A 108 SER A 113 5 6 HELIX 5 5 ALA A 117 ASP A 128 1 12 SHEET 1 A 4 GLU A 14 GLU A 19 0 SHEET 2 A 4 VAL A 22 ILE A 27 -1 N GLY A 26 O TRP A 15 SHEET 3 A 4 ILE A 101 PRO A 105 -1 N ILE A 103 O ALA A 23 SHEET 4 A 4 GLY A 74 VAL A 79 -1 N GLU A 78 O LYS A 102 SHEET 1 B 3 VAL A 38 GLU A 42 0 SHEET 2 B 3 GLY A 55 SER A 61 -1 N GLU A 60 O VAL A 39 SHEET 3 B 3 THR A 65 ASN A 69 -1 N VAL A 68 O PHE A 56 LINK NZ LYS A 63 C1 OSS 63 CRYST1 61.340 55.380 33.770 90.00 90.00 90.00 P 21 21 2 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 0.016303 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018057 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029612 0.00000