HEADER LYASE 27-FEB-17 5X7M TITLE CRYSTAL STRUCTURE OF MESO-DIAMINOPIMELATE DECARBOXYLASE (DAPDC) FROM TITLE 2 CORYNEBACTERIUM GLUTAMICUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIAMINOPIMELATE DECARBOXYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DAPDC; COMPND 5 EC: 4.1.1.20; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM GLUTAMICUM (STRAIN ATCC 13032 / SOURCE 3 DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025); SOURCE 4 ORGANISM_TAXID: 196627; SOURCE 5 STRAIN: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025; SOURCE 6 GENE: LYSA, CGL1180, CG1334; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-T1R; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS DECARBOXYLASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR H.-F.SON,K.-J.KIM REVDAT 3 22-NOV-23 5X7M 1 REMARK REVDAT 2 09-SEP-20 5X7M 1 TITLE REVDAT 1 10-JAN-18 5X7M 0 JRNL AUTH H.F.SON,K.J.KIM JRNL TITL STRUCTURAL BASIS FOR SUBSTRATE SPECIFICITY OF JRNL TITL 2 MESO-DIAMINOPIMELIC ACID DECARBOXYLASE FROM CORYNEBACTERIUM JRNL TITL 3 GLUTAMICUM. JRNL REF BIOCHEM. BIOPHYS. RES. V. 495 1815 2018 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 29233695 JRNL DOI 10.1016/J.BBRC.2017.11.097 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 36222 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1898 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2347 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.3650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6652 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 131 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.63000 REMARK 3 B22 (A**2) : 0.76000 REMARK 3 B33 (A**2) : -0.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.403 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.272 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.196 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.747 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6808 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6380 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9260 ; 1.725 ; 1.962 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14642 ; 1.025 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 884 ; 7.584 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 308 ;37.499 ;24.156 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1042 ;15.097 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;17.033 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1056 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7884 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1522 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES REMARK 4 REMARK 4 5X7M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1300003034. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000, HKL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36222 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 94.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.8800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-2000 REMARK 200 STARTING MODEL: 1HKV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE TRIBASIC, SODIUM REMARK 280 CACODYLATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 57.32500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.00650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 57.32500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.00650 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 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 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 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LEU A 446 REMARK 465 GLU A 447 REMARK 465 HIS A 448 REMARK 465 HIS A 449 REMARK 465 HIS A 450 REMARK 465 HIS A 451 REMARK 465 HIS A 452 REMARK 465 HIS A 453 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 LEU B 446 REMARK 465 GLU B 447 REMARK 465 HIS B 448 REMARK 465 HIS B 449 REMARK 465 HIS B 450 REMARK 465 HIS B 451 REMARK 465 HIS B 452 REMARK 465 HIS B 453 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 DISTANCE REMARK 500 NZ LYS B 75 C4 PLP B 501 2.03 REMARK 500 O PRO B 44 NH1 ARG B 434 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 21 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 330 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 343 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 343 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 417 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 417 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 434 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 434 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 56 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 233 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 233 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 434 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 434 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PHE A 77 132.87 171.20 REMARK 500 ASN A 120 58.47 -150.40 REMARK 500 ASN A 203 -70.03 -65.91 REMARK 500 ASN A 204 -44.04 -24.11 REMARK 500 ARG A 358 166.90 178.02 REMARK 500 ASP A 383 95.64 -166.34 REMARK 500 TYR A 404 -29.83 64.39 REMARK 500 ASP B 49 92.08 -67.16 REMARK 500 LYS B 75 -39.68 -35.25 REMARK 500 PHE B 77 124.79 169.76 REMARK 500 ALA B 96 16.32 -141.91 REMARK 500 ASP B 383 99.66 -162.34 REMARK 500 TYR B 404 -46.05 67.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 156 LYS A 157 -131.43 REMARK 500 GLY B 156 LYS B 157 -139.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP B 501 and LYS B REMARK 800 75 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5X7N RELATED DB: PDB DBREF 5X7M A 1 445 UNP P09890 DCDA_CORGL 1 445 DBREF 5X7M B 1 445 UNP P09890 DCDA_CORGL 1 445 SEQADV 5X7M LEU A 446 UNP P09890 EXPRESSION TAG SEQADV 5X7M GLU A 447 UNP P09890 EXPRESSION TAG SEQADV 5X7M HIS A 448 UNP P09890 EXPRESSION TAG SEQADV 5X7M HIS A 449 UNP P09890 EXPRESSION TAG SEQADV 5X7M HIS A 450 UNP P09890 EXPRESSION TAG SEQADV 5X7M HIS A 451 UNP P09890 EXPRESSION TAG SEQADV 5X7M HIS A 452 UNP P09890 EXPRESSION TAG SEQADV 5X7M HIS A 453 UNP P09890 EXPRESSION TAG SEQADV 5X7M LEU B 446 UNP P09890 EXPRESSION TAG SEQADV 5X7M GLU B 447 UNP P09890 EXPRESSION TAG SEQADV 5X7M HIS B 448 UNP P09890 EXPRESSION TAG SEQADV 5X7M HIS B 449 UNP P09890 EXPRESSION TAG SEQADV 5X7M HIS B 450 UNP P09890 EXPRESSION TAG SEQADV 5X7M HIS B 451 UNP P09890 EXPRESSION TAG SEQADV 5X7M HIS B 452 UNP P09890 EXPRESSION TAG SEQADV 5X7M HIS B 453 UNP P09890 EXPRESSION TAG SEQRES 1 A 453 MET ALA THR VAL GLU ASN PHE ASN GLU LEU PRO ALA HIS SEQRES 2 A 453 VAL TRP PRO ARG ASN ALA VAL ARG GLN GLU ASP GLY VAL SEQRES 3 A 453 VAL THR VAL ALA GLY VAL PRO LEU PRO ASP LEU ALA GLU SEQRES 4 A 453 GLU TYR GLY THR PRO LEU PHE VAL VAL ASP GLU ASP ASP SEQRES 5 A 453 PHE ARG SER ARG CYS ARG ASP MET ALA THR ALA PHE GLY SEQRES 6 A 453 GLY PRO GLY ASN VAL HIS TYR ALA SER LYS ALA PHE LEU SEQRES 7 A 453 THR LYS THR ILE ALA ARG TRP VAL ASP GLU GLU GLY LEU SEQRES 8 A 453 ALA LEU ASP ILE ALA SER ILE ASN GLU LEU GLY ILE ALA SEQRES 9 A 453 LEU ALA ALA GLY PHE PRO ALA SER ARG ILE THR ALA HIS SEQRES 10 A 453 GLY ASN ASN LYS GLY VAL GLU PHE LEU ARG ALA LEU VAL SEQRES 11 A 453 GLN ASN GLY VAL GLY HIS VAL VAL LEU ASP SER ALA GLN SEQRES 12 A 453 GLU LEU GLU LEU LEU ASP TYR VAL ALA ALA GLY GLU GLY SEQRES 13 A 453 LYS ILE GLN ASP VAL LEU ILE ARG VAL LYS PRO GLY ILE SEQRES 14 A 453 GLU ALA HIS THR HIS GLU PHE ILE ALA THR SER HIS GLU SEQRES 15 A 453 ASP GLN LYS PHE GLY PHE SER LEU ALA SER GLY SER ALA SEQRES 16 A 453 PHE GLU ALA ALA LYS ALA ALA ASN ASN ALA GLU ASN LEU SEQRES 17 A 453 ASN LEU VAL GLY LEU HIS CYS HIS VAL GLY SER GLN VAL SEQRES 18 A 453 PHE ASP ALA GLU GLY PHE LYS LEU ALA ALA GLU ARG VAL SEQRES 19 A 453 LEU GLY LEU TYR SER GLN ILE HIS SER GLU LEU GLY VAL SEQRES 20 A 453 ALA LEU PRO GLU LEU ASP LEU GLY GLY GLY TYR GLY ILE SEQRES 21 A 453 ALA TYR THR ALA ALA GLU GLU PRO LEU ASN VAL ALA GLU SEQRES 22 A 453 VAL ALA SER ASP LEU LEU THR ALA VAL GLY LYS MET ALA SEQRES 23 A 453 ALA GLU LEU GLY ILE ASP ALA PRO THR VAL LEU VAL GLU SEQRES 24 A 453 PRO GLY ARG ALA ILE ALA GLY PRO SER THR VAL THR ILE SEQRES 25 A 453 TYR GLU VAL GLY THR THR LYS ASP VAL HIS VAL ASP ASP SEQRES 26 A 453 ASP LYS THR ARG ARG TYR ILE ALA VAL ASP GLY GLY MET SEQRES 27 A 453 SER ASP ASN ILE ARG PRO ALA LEU TYR GLY SER GLU TYR SEQRES 28 A 453 ASP ALA ARG VAL VAL SER ARG PHE ALA GLU GLY ASP PRO SEQRES 29 A 453 VAL SER THR ARG ILE VAL GLY SER HIS CYS GLU SER GLY SEQRES 30 A 453 ASP ILE LEU ILE ASN ASP GLU ILE TYR PRO SER ASP ILE SEQRES 31 A 453 THR SER GLY ASP PHE LEU ALA LEU ALA ALA THR GLY ALA SEQRES 32 A 453 TYR CYS TYR ALA MET SER SER ARG TYR ASN ALA PHE THR SEQRES 33 A 453 ARG PRO ALA VAL VAL SER VAL ARG ALA GLY SER SER ARG SEQRES 34 A 453 LEU MET LEU ARG ARG GLU THR LEU ASP ASP ILE LEU SER SEQRES 35 A 453 LEU GLU ALA LEU GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 453 MET ALA THR VAL GLU ASN PHE ASN GLU LEU PRO ALA HIS SEQRES 2 B 453 VAL TRP PRO ARG ASN ALA VAL ARG GLN GLU ASP GLY VAL SEQRES 3 B 453 VAL THR VAL ALA GLY VAL PRO LEU PRO ASP LEU ALA GLU SEQRES 4 B 453 GLU TYR GLY THR PRO LEU PHE VAL VAL ASP GLU ASP ASP SEQRES 5 B 453 PHE ARG SER ARG CYS ARG ASP MET ALA THR ALA PHE GLY SEQRES 6 B 453 GLY PRO GLY ASN VAL HIS TYR ALA SER LYS ALA PHE LEU SEQRES 7 B 453 THR LYS THR ILE ALA ARG TRP VAL ASP GLU GLU GLY LEU SEQRES 8 B 453 ALA LEU ASP ILE ALA SER ILE ASN GLU LEU GLY ILE ALA SEQRES 9 B 453 LEU ALA ALA GLY PHE PRO ALA SER ARG ILE THR ALA HIS SEQRES 10 B 453 GLY ASN ASN LYS GLY VAL GLU PHE LEU ARG ALA LEU VAL SEQRES 11 B 453 GLN ASN GLY VAL GLY HIS VAL VAL LEU ASP SER ALA GLN SEQRES 12 B 453 GLU LEU GLU LEU LEU ASP TYR VAL ALA ALA GLY GLU GLY SEQRES 13 B 453 LYS ILE GLN ASP VAL LEU ILE ARG VAL LYS PRO GLY ILE SEQRES 14 B 453 GLU ALA HIS THR HIS GLU PHE ILE ALA THR SER HIS GLU SEQRES 15 B 453 ASP GLN LYS PHE GLY PHE SER LEU ALA SER GLY SER ALA SEQRES 16 B 453 PHE GLU ALA ALA LYS ALA ALA ASN ASN ALA GLU ASN LEU SEQRES 17 B 453 ASN LEU VAL GLY LEU HIS CYS HIS VAL GLY SER GLN VAL SEQRES 18 B 453 PHE ASP ALA GLU GLY PHE LYS LEU ALA ALA GLU ARG VAL SEQRES 19 B 453 LEU GLY LEU TYR SER GLN ILE HIS SER GLU LEU GLY VAL SEQRES 20 B 453 ALA LEU PRO GLU LEU ASP LEU GLY GLY GLY TYR GLY ILE SEQRES 21 B 453 ALA TYR THR ALA ALA GLU GLU PRO LEU ASN VAL ALA GLU SEQRES 22 B 453 VAL ALA SER ASP LEU LEU THR ALA VAL GLY LYS MET ALA SEQRES 23 B 453 ALA GLU LEU GLY ILE ASP ALA PRO THR VAL LEU VAL GLU SEQRES 24 B 453 PRO GLY ARG ALA ILE ALA GLY PRO SER THR VAL THR ILE SEQRES 25 B 453 TYR GLU VAL GLY THR THR LYS ASP VAL HIS VAL ASP ASP SEQRES 26 B 453 ASP LYS THR ARG ARG TYR ILE ALA VAL ASP GLY GLY MET SEQRES 27 B 453 SER ASP ASN ILE ARG PRO ALA LEU TYR GLY SER GLU TYR SEQRES 28 B 453 ASP ALA ARG VAL VAL SER ARG PHE ALA GLU GLY ASP PRO SEQRES 29 B 453 VAL SER THR ARG ILE VAL GLY SER HIS CYS GLU SER GLY SEQRES 30 B 453 ASP ILE LEU ILE ASN ASP GLU ILE TYR PRO SER ASP ILE SEQRES 31 B 453 THR SER GLY ASP PHE LEU ALA LEU ALA ALA THR GLY ALA SEQRES 32 B 453 TYR CYS TYR ALA MET SER SER ARG TYR ASN ALA PHE THR SEQRES 33 B 453 ARG PRO ALA VAL VAL SER VAL ARG ALA GLY SER SER ARG SEQRES 34 B 453 LEU MET LEU ARG ARG GLU THR LEU ASP ASP ILE LEU SER SEQRES 35 B 453 LEU GLU ALA LEU GLU HIS HIS HIS HIS HIS HIS HET PLP A 501 15 HET PLP B 501 15 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 5 HOH *131(H2 O) HELIX 1 AA1 THR A 3 ASN A 8 1 6 HELIX 2 AA2 LEU A 34 GLY A 42 1 9 HELIX 3 AA3 GLU A 50 GLY A 65 1 16 HELIX 4 AA4 GLY A 66 ASN A 69 5 4 HELIX 5 AA5 LYS A 75 PHE A 77 5 3 HELIX 6 AA6 THR A 79 GLY A 90 1 12 HELIX 7 AA7 SER A 97 ALA A 107 1 11 HELIX 8 AA8 PRO A 110 SER A 112 5 3 HELIX 9 AA9 GLY A 122 GLY A 133 1 12 HELIX 10 AB1 SER A 141 GLU A 155 1 15 HELIX 11 AB2 GLY A 193 ALA A 205 1 13 HELIX 12 AB3 ALA A 224 GLY A 246 1 23 HELIX 13 AB4 ASN A 270 GLY A 290 1 21 HELIX 14 AB5 GLY A 301 GLY A 306 1 6 HELIX 15 AB6 ILE A 342 GLY A 348 1 7 HELIX 16 AB7 CYS A 405 SER A 409 5 5 HELIX 17 AB8 ARG A 411 PHE A 415 5 5 HELIX 18 AB9 THR A 436 LEU A 443 1 8 HELIX 19 AC1 VAL B 4 GLU B 9 1 6 HELIX 20 AC2 LEU B 34 GLY B 42 1 9 HELIX 21 AC3 GLU B 50 PHE B 64 1 15 HELIX 22 AC4 GLY B 66 ASN B 69 5 4 HELIX 23 AC5 LYS B 75 PHE B 77 5 3 HELIX 24 AC6 THR B 79 GLU B 89 1 11 HELIX 25 AC7 SER B 97 ALA B 107 1 11 HELIX 26 AC8 PRO B 110 SER B 112 5 3 HELIX 27 AC9 GLY B 122 ASN B 132 1 11 HELIX 28 AD1 SER B 141 GLU B 155 1 15 HELIX 29 AD2 GLY B 193 ALA B 205 1 13 HELIX 30 AD3 ALA B 224 GLY B 246 1 23 HELIX 31 AD4 ASN B 270 GLY B 290 1 21 HELIX 32 AD5 GLY B 301 GLY B 306 1 6 HELIX 33 AD6 ILE B 342 GLY B 348 1 7 HELIX 34 AD7 CYS B 405 SER B 409 5 5 HELIX 35 AD8 ARG B 411 PHE B 415 5 5 HELIX 36 AD9 THR B 436 SER B 442 1 7 SHEET 1 AA1 3 ALA A 19 ARG A 21 0 SHEET 2 AA1 3 VAL A 27 VAL A 29 -1 O THR A 28 N VAL A 20 SHEET 3 AA1 3 VAL A 32 PRO A 33 -1 O VAL A 32 N VAL A 29 SHEET 1 AA2 6 ALA A 353 VAL A 355 0 SHEET 2 AA2 6 PHE A 395 ALA A 399 -1 O ALA A 397 N ARG A 354 SHEET 3 AA2 6 THR A 309 HIS A 322 -1 N TYR A 313 O LEU A 396 SHEET 4 AA2 6 THR A 328 VAL A 334 -1 O ARG A 329 N VAL A 321 SHEET 5 AA2 6 PRO A 364 VAL A 370 1 O ARG A 368 N ARG A 330 SHEET 6 AA2 6 ILE A 379 PRO A 387 -1 O LEU A 380 N ILE A 369 SHEET 1 AA3 6 ALA A 353 VAL A 355 0 SHEET 2 AA3 6 PHE A 395 ALA A 399 -1 O ALA A 397 N ARG A 354 SHEET 3 AA3 6 THR A 309 HIS A 322 -1 N TYR A 313 O LEU A 396 SHEET 4 AA3 6 LEU A 45 ASP A 49 -1 N LEU A 45 O ILE A 312 SHEET 5 AA3 6 ALA A 419 ARG A 424 1 O VAL A 421 N PHE A 46 SHEET 6 AA3 6 SER A 427 LEU A 432 -1 O ARG A 429 N SER A 422 SHEET 1 AA4 6 HIS A 71 ALA A 73 0 SHEET 2 AA4 6 ALA A 92 ILE A 95 1 O ALA A 92 N TYR A 72 SHEET 3 AA4 6 ILE A 114 ALA A 116 1 O THR A 115 N ILE A 95 SHEET 4 AA4 6 HIS A 136 LEU A 139 1 O VAL A 138 N ALA A 116 SHEET 5 AA4 6 GLN A 159 LYS A 166 1 O LEU A 162 N LEU A 139 SHEET 6 AA4 6 PHE A 188 SER A 189 1 O PHE A 188 N ARG A 164 SHEET 1 AA5 8 HIS A 71 ALA A 73 0 SHEET 2 AA5 8 ALA A 92 ILE A 95 1 O ALA A 92 N TYR A 72 SHEET 3 AA5 8 ILE A 114 ALA A 116 1 O THR A 115 N ILE A 95 SHEET 4 AA5 8 HIS A 136 LEU A 139 1 O VAL A 138 N ALA A 116 SHEET 5 AA5 8 GLN A 159 LYS A 166 1 O LEU A 162 N LEU A 139 SHEET 6 AA5 8 LEU A 208 HIS A 214 1 O HIS A 214 N VAL A 165 SHEET 7 AA5 8 GLU A 251 ASP A 253 1 O ASP A 253 N LEU A 213 SHEET 8 AA5 8 THR A 295 LEU A 297 1 O LEU A 297 N LEU A 252 SHEET 1 AA6 2 ILE A 169 ALA A 171 0 SHEET 2 AA6 2 PHE A 176 ALA A 178 -1 O ILE A 177 N GLU A 170 SHEET 1 AA7 3 ALA B 19 ARG B 21 0 SHEET 2 AA7 3 VAL B 27 VAL B 29 -1 O THR B 28 N VAL B 20 SHEET 3 AA7 3 VAL B 32 PRO B 33 -1 O VAL B 32 N VAL B 29 SHEET 1 AA8 6 ALA B 353 VAL B 355 0 SHEET 2 AA8 6 PHE B 395 LEU B 398 -1 O ALA B 397 N ARG B 354 SHEET 3 AA8 6 THR B 309 ASP B 324 -1 N TYR B 313 O LEU B 396 SHEET 4 AA8 6 LYS B 327 VAL B 334 -1 O ALA B 333 N GLY B 316 SHEET 5 AA8 6 PRO B 364 VAL B 370 1 O SER B 366 N ARG B 330 SHEET 6 AA8 6 ILE B 379 PRO B 387 -1 O GLU B 384 N THR B 367 SHEET 1 AA9 6 ALA B 353 VAL B 355 0 SHEET 2 AA9 6 PHE B 395 LEU B 398 -1 O ALA B 397 N ARG B 354 SHEET 3 AA9 6 THR B 309 ASP B 324 -1 N TYR B 313 O LEU B 396 SHEET 4 AA9 6 LEU B 45 ASP B 49 -1 N VAL B 47 O VAL B 310 SHEET 5 AA9 6 ALA B 419 ARG B 424 1 O VAL B 423 N VAL B 48 SHEET 6 AA9 6 SER B 427 LEU B 432 -1 O SER B 427 N ARG B 424 SHEET 1 AB1 6 HIS B 71 ALA B 73 0 SHEET 2 AB1 6 ALA B 92 ILE B 95 1 O ASP B 94 N TYR B 72 SHEET 3 AB1 6 ILE B 114 ALA B 116 1 O THR B 115 N LEU B 93 SHEET 4 AB1 6 HIS B 136 LEU B 139 1 O VAL B 138 N ALA B 116 SHEET 5 AB1 6 GLN B 159 LYS B 166 1 O LEU B 162 N LEU B 139 SHEET 6 AB1 6 PHE B 188 SER B 189 1 O PHE B 188 N LYS B 166 SHEET 1 AB2 8 HIS B 71 ALA B 73 0 SHEET 2 AB2 8 ALA B 92 ILE B 95 1 O ASP B 94 N TYR B 72 SHEET 3 AB2 8 ILE B 114 ALA B 116 1 O THR B 115 N LEU B 93 SHEET 4 AB2 8 HIS B 136 LEU B 139 1 O VAL B 138 N ALA B 116 SHEET 5 AB2 8 GLN B 159 LYS B 166 1 O LEU B 162 N LEU B 139 SHEET 6 AB2 8 LEU B 208 HIS B 214 1 O HIS B 214 N ILE B 163 SHEET 7 AB2 8 GLU B 251 ASP B 253 1 O ASP B 253 N LEU B 213 SHEET 8 AB2 8 THR B 295 LEU B 297 1 O LEU B 297 N LEU B 252 SHEET 1 AB3 2 ILE B 169 ALA B 171 0 SHEET 2 AB3 2 PHE B 176 ALA B 178 -1 O ILE B 177 N GLU B 170 LINK NZ LYS A 75 C4A PLP A 501 1555 1555 1.29 LINK NZ LYS B 75 C4A PLP B 501 1555 1555 1.27 CISPEP 1 THR A 43 PRO A 44 0 3.93 CISPEP 2 THR B 43 PRO B 44 0 2.03 SITE 1 AC1 12 LYS A 75 HIS A 117 ARG A 164 HIS A 216 SITE 2 AC1 12 GLY A 256 GLY A 257 GLU A 299 GLY A 301 SITE 3 AC1 12 ARG A 302 TYR A 404 HOH A 605 CYS B 374 SITE 1 AC2 16 CYS A 374 TYR A 412 ALA B 73 SER B 74 SITE 2 AC2 16 ALA B 76 PHE B 77 ASP B 94 GLU B 100 SITE 3 AC2 16 HIS B 117 HIS B 216 GLY B 256 GLY B 257 SITE 4 AC2 16 GLU B 299 GLY B 301 ARG B 302 TYR B 404 CRYST1 114.650 92.013 94.753 90.00 90.00 90.00 P 21 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 0.008722 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010554 0.00000