HEADER TRANSFERASE 13-JUN-16 5B87 TITLE CRYSTAL STRUCTURE OF A CYSTEINE DESULFURASE FROM THERMOCOCCUS TITLE 2 ONNURINEUS NA1 IN COMPLEX WITH ALANINE AT 2.3 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINE DESULFURASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.8.1.7; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS ONNURINEUS (STRAIN NA1); SOURCE 3 ORGANISM_TAXID: 523850; SOURCE 4 STRAIN: NA1; SOURCE 5 GENE: TON_0289; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS CYSTEINE DESULFURASE, CYSTEINE TRASFERASES, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.-H.HO,L.-W.KANG REVDAT 4 15-NOV-23 5B87 1 REMARK REVDAT 3 08-NOV-23 5B87 1 LINK REVDAT 2 13-JUN-18 5B87 1 JRNL REVDAT 1 14-JUN-17 5B87 0 JRNL AUTH T.-H.HO,K.-H.HUYNH,D.Q.NGUYEN,H.PARK,K.JUNG,B.SUR,Y.-J.AHN, JRNL AUTH 2 S.-S.CHA,L.-W.KANG JRNL TITL CATALYTIC INTERMEDIATE CRYSTAL STRUCTURES OF CYSTEINE JRNL TITL 2 DESULFURASE FROM THE ARCHAEONTHERMOCOCCUS ONNURINEUS NA1. JRNL REF ARCHAEA V.2017 95293 2017 JRNL REFN ESSN 1472-3654 JRNL PMID 28536498 JRNL DOI 10.1155/2017/5395293 REMARK 2 REMARK 2 RESOLUTION. 2.28 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) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 38845 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2040 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) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2915 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.2580 REMARK 3 BIN FREE R VALUE SET COUNT : 148 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6218 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 137 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.25000 REMARK 3 B22 (A**2) : 4.47000 REMARK 3 B33 (A**2) : -4.21000 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): 0.299 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.222 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.149 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.143 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.934 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6396 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6182 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8645 ; 2.030 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14256 ; 1.246 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 796 ; 6.897 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 284 ;36.107 ;24.085 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1105 ;20.714 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;15.378 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 959 ; 0.161 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7154 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1404 ; 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): 3196 ; 3.452 ; 3.992 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3196 ; 3.451 ; 3.992 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3988 ; 4.910 ; 5.966 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3989 ; 4.910 ; 5.967 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3200 ; 4.479 ; 4.517 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3196 ; 4.480 ; 4.520 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4652 ; 6.809 ; 6.557 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7045 ; 8.404 ;31.344 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7037 ; 8.405 ;31.335 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 REMARK 4 REMARK 4 5B87 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000694. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUL-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : DCM SI (111) CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40955 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 5B7S REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.03 M MGCL2, 0.03 M CACL2, 15% (V/V) REMARK 280 GLYCEROL, 15% (W/V) PEG 4000, 5MM L-ALANINE, 1MM PLP AND 0.1 M REMARK 280 TRIS (BASE)/ BICINE PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 33.64100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.76700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.90450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 72.76700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.64100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.90450 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: 8230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 SER A -12 REMARK 465 SER A -11 REMARK 465 GLU A -10 REMARK 465 ASN A -9 REMARK 465 LEU A -8 REMARK 465 TYR A -7 REMARK 465 PHE A -6 REMARK 465 GLN A -5 REMARK 465 GLY A -4 REMARK 465 HIS A -3 REMARK 465 MET A -2 REMARK 465 ALA A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 THR A 399 REMARK 465 MET B -19 REMARK 465 HIS B -18 REMARK 465 HIS B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 SER B -12 REMARK 465 SER B -11 REMARK 465 GLU B -10 REMARK 465 ASN B -9 REMARK 465 LEU B -8 REMARK 465 TYR B -7 REMARK 465 PHE B -6 REMARK 465 GLN B -5 REMARK 465 GLY B -4 REMARK 465 HIS B -3 REMARK 465 THR B 399 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE A 107 CG1 CG2 CD1 REMARK 470 LYS A 127 CG CD CE NZ REMARK 470 LYS A 153 CG CD CE NZ REMARK 470 LYS A 181 CG CD CE NZ 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 PRO A 4 C - N - CD ANGL. DEV. = 16.5 DEGREES REMARK 500 PRO B 4 C - N - CD ANGL. DEV. = 15.6 DEGREES REMARK 500 ARG B 318 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 LEU B 393 CA - CB - CG ANGL. DEV. = 15.7 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 THR A 25 149.14 -172.34 REMARK 500 VAL A 47 -126.48 -98.62 REMARK 500 HIS A 48 -132.56 57.52 REMARK 500 PHE A 77 -61.05 -25.09 REMARK 500 LEU A 118 -60.16 -131.97 REMARK 500 LYS A 216 -124.15 -95.70 REMARK 500 ALA A 357 51.83 -141.00 REMARK 500 THR B 25 149.13 -176.55 REMARK 500 TYR B 43 40.59 -142.15 REMARK 500 VAL B 47 -131.82 -93.53 REMARK 500 ARG B 49 42.33 38.62 REMARK 500 LEU B 118 -65.78 -134.20 REMARK 500 LYS B 216 -124.33 -90.65 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 Di-peptide PLP A 400 and ALA A REMARK 800 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP B 400 and ALA B REMARK 800 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP B 400 and LYS B REMARK 800 216 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5B7S RELATED DB: PDB REMARK 900 RELATED ID: 5B7U RELATED DB: PDB REMARK 900 RELATED ID: 5B89 RELATED DB: PDB DBREF 5B87 A 1 399 UNP B6YT87 B6YT87_THEON 1 399 DBREF 5B87 B 1 399 UNP B6YT87 B6YT87_THEON 1 399 SEQADV 5B87 MET A -19 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS A -18 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS A -17 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS A -16 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS A -15 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS A -14 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS A -13 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 SER A -12 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 SER A -11 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 GLU A -10 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 ASN A -9 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 LEU A -8 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 TYR A -7 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 PHE A -6 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 GLN A -5 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 GLY A -4 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS A -3 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 MET A -2 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 ALA A -1 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 SER A 0 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 MET B -19 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS B -18 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS B -17 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS B -16 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS B -15 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS B -14 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS B -13 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 SER B -12 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 SER B -11 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 GLU B -10 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 ASN B -9 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 LEU B -8 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 TYR B -7 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 PHE B -6 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 GLN B -5 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 GLY B -4 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 HIS B -3 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 MET B -2 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 ALA B -1 UNP B6YT87 EXPRESSION TAG SEQADV 5B87 SER B 0 UNP B6YT87 EXPRESSION TAG SEQRES 1 A 419 MET HIS HIS HIS HIS HIS HIS SER SER GLU ASN LEU TYR SEQRES 2 A 419 PHE GLN GLY HIS MET ALA SER MET ARG ILE PRO GLU ASP SEQRES 3 A 419 VAL ARG LYS ASP ILE PRO LEU THR ASN GLU VAL ILE TYR SEQRES 4 A 419 PHE ASP ASN THR ALA THR SER LEU THR PRO LYS PRO VAL SEQRES 5 A 419 VAL GLU ALA MET ASP GLU TYR TYR LEU LYS TYR ARG ALA SEQRES 6 A 419 ASN VAL HIS ARG GLY VAL HIS ARG LEU SER GLN MET ALA SEQRES 7 A 419 THR HIS LYS TYR GLU GLU SER ARG LYS ILE VAL ALA ASP SEQRES 8 A 419 PHE ILE GLY ALA LYS PHE GLU GLU ILE VAL PHE THR LYS SEQRES 9 A 419 ASN THR SER GLU SER LEU ASN LEU VAL ALA LEU GLY LEU SEQRES 10 A 419 GLY HIS ILE PHE LYS ARG GLY ASP LYS ILE VAL THR THR SEQRES 11 A 419 PRO TYR GLU HIS HIS SER ASP LEU LEU PRO TRP GLN ARG SEQRES 12 A 419 LEU ALA THR LYS LEU GLY LEU LYS LEU GLU PHE ILE GLU SEQRES 13 A 419 GLY ASP ASP GLU GLY ASN LEU ASP LEU SER ASP ALA GLU SEQRES 14 A 419 LYS LYS ILE LYS GLY ALA LYS LEU VAL ALA VAL GLN HIS SEQRES 15 A 419 VAL SER ASN ALA LEU GLY VAL ILE HIS GLU VAL GLU GLU SEQRES 16 A 419 LEU GLY LYS ILE ALA LYS ASP GLU GLY ALA ILE PHE VAL SEQRES 17 A 419 VAL ASP ALA ALA GLN SER ALA GLY HIS MET GLU VAL ASN SEQRES 18 A 419 VAL LYS LYS LEU HIS ALA ASP PHE LEU ALA PHE SER GLY SEQRES 19 A 419 HIS LYS GLY PRO MET GLY PRO THR GLY ILE GLY VAL LEU SEQRES 20 A 419 TYR ILE ARG GLU GLU PHE PHE ASP THR PHE GLU PRO PRO SEQRES 21 A 419 LEU ILE GLY GLY GLY THR ILE GLU ASP VAL SER LEU ASP SEQRES 22 A 419 GLY TYR LYS LEU THR GLU PRO PRO GLU ARG PHE GLU ALA SEQRES 23 A 419 GLY THR PRO ASN ILE GLY GLY ALA ILE GLY LEU ALA ALA SEQRES 24 A 419 GLY ILE ARG TYR ILE GLU ARG ILE GLY LEU GLY ARG ILE SEQRES 25 A 419 GLU ARG GLN GLU HIS LYS LEU VAL LYS ARG THR THR GLU SEQRES 26 A 419 GLY LEU ASP GLU LEU GLU VAL PRO TRP TYR GLY PRO ARG SEQRES 27 A 419 ASN LEU LYS LYS HIS ALA GLY VAL VAL SER PHE ASN VAL SEQRES 28 A 419 PRO GLY LEU HIS PRO HIS ASP VAL ALA ALA ILE LEU ASP SEQRES 29 A 419 ASP HIS SER ILE MET VAL ARG SER GLY HIS HIS CSS ALA SEQRES 30 A 419 LEU PRO VAL MET LYS LYS LEU GLY ILE ASN GLY THR VAL SEQRES 31 A 419 ARG ALA SER PHE HIS VAL TYR ASN SER LEU GLU GLU VAL SEQRES 32 A 419 GLU THR PHE LEU GLY VAL MET GLU GLU LEU VAL LYS GLY SEQRES 33 A 419 LEU LYS THR SEQRES 1 B 419 MET HIS HIS HIS HIS HIS HIS SER SER GLU ASN LEU TYR SEQRES 2 B 419 PHE GLN GLY HIS MET ALA SER MET ARG ILE PRO GLU ASP SEQRES 3 B 419 VAL ARG LYS ASP ILE PRO LEU THR ASN GLU VAL ILE TYR SEQRES 4 B 419 PHE ASP ASN THR ALA THR SER LEU THR PRO LYS PRO VAL SEQRES 5 B 419 VAL GLU ALA MET ASP GLU TYR TYR LEU LYS TYR ARG ALA SEQRES 6 B 419 ASN VAL HIS ARG GLY VAL HIS ARG LEU SER GLN MET ALA SEQRES 7 B 419 THR HIS LYS TYR GLU GLU SER ARG LYS ILE VAL ALA ASP SEQRES 8 B 419 PHE ILE GLY ALA LYS PHE GLU GLU ILE VAL PHE THR LYS SEQRES 9 B 419 ASN THR SER GLU SER LEU ASN LEU VAL ALA LEU GLY LEU SEQRES 10 B 419 GLY HIS ILE PHE LYS ARG GLY ASP LYS ILE VAL THR THR SEQRES 11 B 419 PRO TYR GLU HIS HIS SER ASP LEU LEU PRO TRP GLN ARG SEQRES 12 B 419 LEU ALA THR LYS LEU GLY LEU LYS LEU GLU PHE ILE GLU SEQRES 13 B 419 GLY ASP ASP GLU GLY ASN LEU ASP LEU SER ASP ALA GLU SEQRES 14 B 419 LYS LYS ILE LYS GLY ALA LYS LEU VAL ALA VAL GLN HIS SEQRES 15 B 419 VAL SER ASN ALA LEU GLY VAL ILE HIS GLU VAL GLU GLU SEQRES 16 B 419 LEU GLY LYS ILE ALA LYS ASP GLU GLY ALA ILE PHE VAL SEQRES 17 B 419 VAL ASP ALA ALA GLN SER ALA GLY HIS MET GLU VAL ASN SEQRES 18 B 419 VAL LYS LYS LEU HIS ALA ASP PHE LEU ALA PHE SER GLY SEQRES 19 B 419 HIS LYS GLY PRO MET GLY PRO THR GLY ILE GLY VAL LEU SEQRES 20 B 419 TYR ILE ARG GLU GLU PHE PHE ASP THR PHE GLU PRO PRO SEQRES 21 B 419 LEU ILE GLY GLY GLY THR ILE GLU ASP VAL SER LEU ASP SEQRES 22 B 419 GLY TYR LYS LEU THR GLU PRO PRO GLU ARG PHE GLU ALA SEQRES 23 B 419 GLY THR PRO ASN ILE GLY GLY ALA ILE GLY LEU ALA ALA SEQRES 24 B 419 GLY ILE ARG TYR ILE GLU ARG ILE GLY LEU GLY ARG ILE SEQRES 25 B 419 GLU ARG GLN GLU HIS LYS LEU VAL LYS ARG THR THR GLU SEQRES 26 B 419 GLY LEU ASP GLU LEU GLU VAL PRO TRP TYR GLY PRO ARG SEQRES 27 B 419 ASN LEU LYS LYS HIS ALA GLY VAL VAL SER PHE ASN VAL SEQRES 28 B 419 PRO GLY LEU HIS PRO HIS ASP VAL ALA ALA ILE LEU ASP SEQRES 29 B 419 ASP HIS SER ILE MET VAL ARG SER GLY HIS HIS CSS ALA SEQRES 30 B 419 LEU PRO VAL MET LYS LYS LEU GLY ILE ASN GLY THR VAL SEQRES 31 B 419 ARG ALA SER PHE HIS VAL TYR ASN SER LEU GLU GLU VAL SEQRES 32 B 419 GLU THR PHE LEU GLY VAL MET GLU GLU LEU VAL LYS GLY SEQRES 33 B 419 LEU LYS THR MODRES 5B87 CSS A 356 CYS MODIFIED RESIDUE MODRES 5B87 CSS B 356 CYS MODIFIED RESIDUE HET CSS A 356 7 HET CSS B 356 7 HET PLP A 400 15 HET ALA A 401 6 HET PLP B 400 15 HET ALA B 401 6 HETNAM CSS S-MERCAPTOCYSTEINE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM ALA ALANINE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 1 CSS 2(C3 H7 N O2 S2) FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 4 ALA 2(C3 H7 N O2) FORMUL 7 HOH *137(H2 O) HELIX 1 AA1 PRO A 4 LYS A 9 1 6 HELIX 2 AA2 ASP A 10 GLU A 16 5 7 HELIX 3 AA3 PRO A 29 TYR A 43 1 15 HELIX 4 AA4 HIS A 52 ILE A 73 1 22 HELIX 5 AA5 LYS A 76 GLU A 78 5 3 HELIX 6 AA6 ASN A 85 GLY A 98 1 14 HELIX 7 AA7 HIS A 99 PHE A 101 5 3 HELIX 8 AA8 HIS A 114 ASP A 117 5 4 HELIX 9 AA9 LEU A 118 GLY A 129 1 12 HELIX 10 AB1 ASP A 144 LYS A 153 1 10 HELIX 11 AB2 GLU A 172 GLU A 183 1 12 HELIX 12 AB3 ASN A 201 HIS A 206 1 6 HELIX 13 AB4 GLU A 231 PHE A 234 5 4 HELIX 14 AB5 PRO A 261 GLU A 265 5 5 HELIX 15 AB6 ASN A 270 GLY A 288 1 19 HELIX 16 AB7 GLY A 288 LEU A 310 1 23 HELIX 17 AB8 ASN A 319 HIS A 323 5 5 HELIX 18 AB9 HIS A 335 HIS A 346 1 12 HELIX 19 AC1 ALA A 357 GLY A 365 1 9 HELIX 20 AC2 SER A 379 LEU A 397 1 19 HELIX 21 AC3 PRO B 4 LYS B 9 1 6 HELIX 22 AC4 ASP B 10 GLU B 16 5 7 HELIX 23 AC5 PRO B 29 TYR B 43 1 15 HELIX 24 AC6 HIS B 52 GLY B 74 1 23 HELIX 25 AC7 LYS B 76 GLU B 78 5 3 HELIX 26 AC8 ASN B 85 GLY B 98 1 14 HELIX 27 AC9 HIS B 99 PHE B 101 5 3 HELIX 28 AD1 HIS B 114 ASP B 117 5 4 HELIX 29 AD2 LEU B 118 GLY B 129 1 12 HELIX 30 AD3 ASP B 144 LYS B 153 1 10 HELIX 31 AD4 GLU B 172 GLY B 184 1 13 HELIX 32 AD5 GLU B 231 PHE B 234 5 4 HELIX 33 AD6 PRO B 261 GLU B 265 5 5 HELIX 34 AD7 ASN B 270 GLY B 288 1 19 HELIX 35 AD8 GLY B 288 LEU B 310 1 23 HELIX 36 AD9 ASN B 319 HIS B 323 5 5 HELIX 37 AE1 HIS B 335 HIS B 346 1 12 HELIX 38 AE2 ALA B 357 GLY B 365 1 9 HELIX 39 AE3 SER B 379 VAL B 394 1 16 SHEET 1 AA1 2 ILE A 18 TYR A 19 0 SHEET 2 AA1 2 ILE A 348 MET A 349 1 O MET A 349 N ILE A 18 SHEET 1 AA2 7 ILE A 80 THR A 83 0 SHEET 2 AA2 7 GLY A 225 ILE A 229 -1 O GLY A 225 N THR A 83 SHEET 3 AA2 7 PHE A 209 SER A 213 -1 N LEU A 210 O TYR A 228 SHEET 4 AA2 7 ILE A 186 ASP A 190 1 N VAL A 189 O PHE A 209 SHEET 5 AA2 7 LEU A 157 GLN A 161 1 N VAL A 158 O VAL A 188 SHEET 6 AA2 7 LYS A 106 THR A 109 1 N VAL A 108 O ALA A 159 SHEET 7 AA2 7 LYS A 131 PHE A 134 1 O LYS A 131 N ILE A 107 SHEET 1 AA3 2 ILE A 247 SER A 251 0 SHEET 2 AA3 2 GLY A 254 LEU A 257 -1 O LYS A 256 N GLU A 248 SHEET 1 AA4 3 VAL A 326 PHE A 329 0 SHEET 2 AA4 3 THR A 369 SER A 373 -1 O ALA A 372 N VAL A 327 SHEET 3 AA4 3 ARG A 351 GLY A 353 -1 N ARG A 351 O ARG A 371 SHEET 1 AA5 2 ILE B 18 TYR B 19 0 SHEET 2 AA5 2 ILE B 348 MET B 349 1 O MET B 349 N ILE B 18 SHEET 1 AA6 7 ILE B 80 THR B 83 0 SHEET 2 AA6 7 GLY B 225 ILE B 229 -1 O GLY B 225 N THR B 83 SHEET 3 AA6 7 PHE B 209 SER B 213 -1 N LEU B 210 O TYR B 228 SHEET 4 AA6 7 ILE B 186 ASP B 190 1 N VAL B 189 O ALA B 211 SHEET 5 AA6 7 LEU B 157 GLN B 161 1 N VAL B 158 O ILE B 186 SHEET 6 AA6 7 LYS B 106 THR B 109 1 N VAL B 108 O LEU B 157 SHEET 7 AA6 7 LYS B 131 PHE B 134 1 O LYS B 131 N ILE B 107 SHEET 1 AA7 2 ILE B 247 VAL B 250 0 SHEET 2 AA7 2 TYR B 255 LEU B 257 -1 O LYS B 256 N GLU B 248 SHEET 1 AA8 3 VAL B 326 PHE B 329 0 SHEET 2 AA8 3 THR B 369 SER B 373 -1 O VAL B 370 N PHE B 329 SHEET 3 AA8 3 ARG B 351 GLY B 353 -1 N ARG B 351 O ARG B 371 LINK NZ LYS A 216 C4A PLP A 400 1555 1555 1.47 LINK C HIS A 355 N CSS A 356 1555 1555 1.31 LINK C CSS A 356 N ALA A 357 1555 1555 1.32 LINK C4A PLP A 400 N ALA A 401 1555 1555 1.51 LINK NZ LYS B 216 C4A PLP B 400 1555 1555 1.51 LINK C HIS B 355 N CSS B 356 1555 1555 1.32 LINK C CSS B 356 N ALA B 357 1555 1555 1.31 LINK C4A PLP B 400 N ALA B 401 1555 1555 1.53 CISPEP 1 ILE A 3 PRO A 4 0 1.72 CISPEP 2 GLU A 140 GLY A 141 0 -2.64 CISPEP 3 PRO A 260 PRO A 261 0 -0.36 CISPEP 4 ILE B 3 PRO B 4 0 2.13 CISPEP 5 PRO B 260 PRO B 261 0 1.01 SITE 1 AC1 18 THR A 23 ALA A 24 ASN A 85 THR A 86 SITE 2 AC1 18 SER A 87 HIS A 114 ASN A 165 ASP A 190 SITE 3 AC1 18 ALA A 192 GLN A 193 SER A 213 HIS A 215 SITE 4 AC1 18 LYS A 216 ARG A 371 HOH A 536 ASN B 46 SITE 5 AC1 18 GLY B 267 THR B 268 SITE 1 AC2 18 GLY A 267 THR A 268 THR B 23 ALA B 24 SITE 2 AC2 18 ASN B 85 THR B 86 SER B 87 HIS B 114 SITE 3 AC2 18 ASN B 165 ASP B 190 ALA B 192 GLN B 193 SITE 4 AC2 18 SER B 213 HIS B 215 LYS B 216 HIS B 355 SITE 5 AC2 18 ARG B 371 HOH B 540 SITE 1 AC3 20 GLY A 267 THR A 268 THR B 23 SER B 26 SITE 2 AC3 20 ASN B 85 THR B 86 SER B 87 HIS B 114 SITE 3 AC3 20 ASN B 165 ASP B 190 ALA B 192 GLN B 193 SITE 4 AC3 20 SER B 213 GLY B 214 HIS B 215 GLY B 217 SITE 5 AC3 20 PRO B 218 MET B 219 ALA B 401 HOH B 540 CRYST1 67.282 93.809 145.534 90.00 90.00 90.00 P 21 21 21 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 0.014863 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010660 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006871 0.00000