HEADER TRANSFERASE 06-JUL-16 5KR3 TITLE DIRECTED EVOLUTION OF TRANSAMINASES BY ANCESTRAL RECONSTRUCTION. USING TITLE 2 OLD PROTEINS FOR NEW CHEMISTRIES COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-AMINOBUTYRATE TRANSAMINASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.6.1.18; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS; SOURCE 3 ORGANISM_TAXID: 286; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET KEYWDS PHYLOGENETICS, DIRECTED EVOLUTION, TRANSAMINASE, PROTEIN ENGINEERING, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.WILDING,J.NEWMAN,T.S.PEAT,C.SCOTT REVDAT 3 04-OCT-23 5KR3 1 REMARK REVDAT 2 30-JAN-19 5KR3 1 JRNL REVDAT 1 12-JUL-17 5KR3 0 JRNL AUTH M.WILDING,T.S.PEAT,S.KALYAANAMOORTHY,J.NEWMAN,C.SCOTT, JRNL AUTH 2 L.S.JERMIIN JRNL TITL REVERSE ENGINEERING: TRANSAMINASE BIOCATALYST DEVELOPMENT JRNL TITL 2 USING ANCESTRAL SEQUENCE RECONSTRUCTION JRNL REF GREEN CHEMISTRY V. 19 5375 2017 JRNL DOI 10.1039/C7GC02343J REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 58359 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3091 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3768 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.3600 REMARK 3 BIN FREE R VALUE SET COUNT : 198 REMARK 3 BIN FREE R VALUE : 0.4120 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7006 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 446 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.09000 REMARK 3 B22 (A**2) : -1.70000 REMARK 3 B33 (A**2) : 0.43000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.97000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.227 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.186 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.113 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.033 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.886 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.844 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7257 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6857 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9855 ; 1.563 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15776 ; 0.994 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 923 ; 6.252 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 317 ;32.179 ;23.628 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1156 ;12.960 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 43 ;18.560 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1060 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8306 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1653 ; 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): 3686 ; 1.077 ; 1.691 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3685 ; 1.077 ; 1.691 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4611 ; 1.578 ; 2.529 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4612 ; 1.578 ; 2.530 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3571 ; 1.683 ; 1.912 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3572 ; 1.682 ; 1.912 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5245 ; 2.587 ; 2.793 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 31228 ; 4.062 ;32.635 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 30951 ; 4.031 ;32.595 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 2 459 B 2 459 29514 0.06 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5KR3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222637. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-14 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 : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95370 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63517 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 41.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.66500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5KQT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150 PLUS 150 NL DROPS WITH PROTEIN AT REMARK 280 10 MG/ML AND RESERVOIR CONDITIONS OF 20% PEG 3350, 135 MM REMARK 280 AMMONIUM FORMATE. MICROSEEDS WERE USED FOR NUCLEATION., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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,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 61.08100 REMARK 290 SMTRY3 2 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: 11950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -84.0 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 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 ALA A 193 REMARK 465 GLY A 194 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 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 HIS A 0 CG ND1 CD2 CE1 NE2 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 190 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 345 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ASP A 354 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG B 33 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 345 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG B 345 NE - CZ - NH2 ANGL. DEV. = -3.0 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 SER A 19 59.31 36.61 REMARK 500 HIS A 21 107.45 -48.72 REMARK 500 LEU A 81 99.22 -162.92 REMARK 500 SER A 148 -168.33 -121.66 REMARK 500 ARG A 151 -0.64 71.00 REMARK 500 ILE A 234 70.89 55.58 REMARK 500 ALA A 287 -140.95 -163.01 REMARK 500 LYS A 288 -90.30 37.66 REMARK 500 MET A 381 36.40 -95.93 REMARK 500 SER B 19 62.55 33.12 REMARK 500 HIS B 21 108.76 -49.01 REMARK 500 LEU B 81 98.74 -162.65 REMARK 500 SER B 148 -168.18 -121.38 REMARK 500 ALA B 287 -139.98 -162.26 REMARK 500 LYS B 288 -92.66 37.92 REMARK 500 MET B 381 34.55 -94.94 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 TYR A 83 TYR A 84 148.19 REMARK 500 TYR B 83 TYR B 84 146.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 817 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH B 818 DISTANCE = 7.47 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PLP A 500 REMARK 610 PLP B 500 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 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP B 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KQT RELATED DB: PDB REMARK 900 RELATED ID: 5KQU RELATED DB: PDB REMARK 900 RELATED ID: 5KQV RELATED DB: PDB REMARK 900 RELATED ID: 5KR4 RELATED DB: PDB REMARK 900 RELATED ID: 5KR5 RELATED DB: PDB REMARK 900 RELATED ID: 5KR6 RELATED DB: PDB DBREF 5KR3 A -19 459 PDB 5KR3 5KR3 -19 459 DBREF 5KR3 B -19 459 PDB 5KR3 5KR3 -19 459 SEQRES 1 A 479 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 479 LEU VAL PRO ARG GLY SER HIS MET GLN SER LEU ASP GLN SEQRES 3 A 479 LEU PHE GLU MET ASP ARG ALA HIS PHE MET HIS PRO SER SEQRES 4 A 479 THR HIS ALA HIS ASP HIS ALA SER GLY ALA LEU PRO GLY SEQRES 5 A 479 ARG ILE ILE THR GLY GLY LYS GLY ILE ARG ILE GLU ASP SEQRES 6 A 479 HIS GLU GLY ARG GLU TYR ILE ASP ALA PHE ALA GLY LEU SEQRES 7 A 479 TYR CYS VAL ASN ILE GLY TYR GLY ARG THR GLU VAL ALA SEQRES 8 A 479 ASP ALA ILE TYR GLU GLN ALA LYS GLN LEU ALA TYR TYR SEQRES 9 A 479 HIS THR TYR VAL GLY HIS SER THR ASP ALA ILE ILE GLU SEQRES 10 A 479 LEU SER SER ARG ILE ILE ARG ASP TRP ALA PRO ALA GLY SEQRES 11 A 479 MET LYS LYS VAL TYR TYR GLY MET SER GLY SER ASP ALA SEQRES 12 A 479 ASN GLU THR GLN ILE LYS LEU VAL TRP TYR TYR ASN ASN SEQRES 13 A 479 VAL LEU GLY ARG PRO ASN LYS LYS LYS ILE ILE SER ARG SEQRES 14 A 479 GLU ARG GLY TYR HIS GLY SER GLY ILE VAL THR GLY SER SEQRES 15 A 479 LEU THR GLY LEU PRO SER PHE HIS GLN HIS PHE ASP LEU SEQRES 16 A 479 PRO ILE ASP ARG VAL LYS HIS THR VAL CYS PRO HIS TRP SEQRES 17 A 479 TYR ARG ALA PRO ALA GLY MET SER GLU ALA GLN PHE VAL SEQRES 18 A 479 ALA TYR CYS VAL GLU GLU LEU GLU LYS LEU ILE ALA ARG SEQRES 19 A 479 GLU GLY ALA ASP THR ILE ALA ALA PHE ILE ALA GLU PRO SEQRES 20 A 479 VAL MET GLY THR GLY GLY ILE ILE PRO PRO PRO GLN GLY SEQRES 21 A 479 TYR TRP GLU ALA ILE GLN ALA VAL LEU ARG LYS HIS ASP SEQRES 22 A 479 ILE LEU LEU ILE ALA ASP GLU VAL VAL CYS GLY PHE GLY SEQRES 23 A 479 ARG LEU GLY SER LYS MET GLY SER GLN HIS TYR GLY ILE SEQRES 24 A 479 LYS PRO ASP LEU ILE THR VAL ALA LYS GLY LEU THR SER SEQRES 25 A 479 ALA TYR ALA PRO LEU SER GLY VAL ILE VAL GLY GLU LYS SEQRES 26 A 479 VAL TRP ASP VAL ILE GLU LYS GLY SER GLN GLU HIS GLY SEQRES 27 A 479 PRO MET GLY HIS GLY TRP THR TYR SER GLY HIS PRO ILE SEQRES 28 A 479 CYS ALA ALA ALA ALA LEU ALA ASN LEU ASP ILE LEU GLU SEQRES 29 A 479 ARG GLU ASN LEU THR GLY ASN ALA ALA ASP VAL GLY ALA SEQRES 30 A 479 TYR LEU GLN GLN ARG LEU HIS GLU ALA PHE GLY ALA HIS SEQRES 31 A 479 PRO LEU VAL GLY GLU VAL ARG GLY VAL GLY MET LEU ALA SEQRES 32 A 479 ALA LEU GLU PHE MET ALA ASP LYS ASP ALA ARG THR PRO SEQRES 33 A 479 PHE ASP PRO ALA LEU LYS VAL GLY PRO LYS VAL SER ALA SEQRES 34 A 479 ALA ALA LEU GLU ASP GLY MET ILE ALA ARG ALA MET PRO SEQRES 35 A 479 HIS GLY ASP ILE LEU GLY PHE ALA PRO PRO LEU VAL THR SEQRES 36 A 479 THR ARG ALA GLU VAL ASP GLU ILE VAL GLY ILE ALA LYS SEQRES 37 A 479 GLN ALA VAL ASP GLU VAL ALA ASP GLU VAL LEU SEQRES 1 B 479 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 479 LEU VAL PRO ARG GLY SER HIS MET GLN SER LEU ASP GLN SEQRES 3 B 479 LEU PHE GLU MET ASP ARG ALA HIS PHE MET HIS PRO SER SEQRES 4 B 479 THR HIS ALA HIS ASP HIS ALA SER GLY ALA LEU PRO GLY SEQRES 5 B 479 ARG ILE ILE THR GLY GLY LYS GLY ILE ARG ILE GLU ASP SEQRES 6 B 479 HIS GLU GLY ARG GLU TYR ILE ASP ALA PHE ALA GLY LEU SEQRES 7 B 479 TYR CYS VAL ASN ILE GLY TYR GLY ARG THR GLU VAL ALA SEQRES 8 B 479 ASP ALA ILE TYR GLU GLN ALA LYS GLN LEU ALA TYR TYR SEQRES 9 B 479 HIS THR TYR VAL GLY HIS SER THR ASP ALA ILE ILE GLU SEQRES 10 B 479 LEU SER SER ARG ILE ILE ARG ASP TRP ALA PRO ALA GLY SEQRES 11 B 479 MET LYS LYS VAL TYR TYR GLY MET SER GLY SER ASP ALA SEQRES 12 B 479 ASN GLU THR GLN ILE LYS LEU VAL TRP TYR TYR ASN ASN SEQRES 13 B 479 VAL LEU GLY ARG PRO ASN LYS LYS LYS ILE ILE SER ARG SEQRES 14 B 479 GLU ARG GLY TYR HIS GLY SER GLY ILE VAL THR GLY SER SEQRES 15 B 479 LEU THR GLY LEU PRO SER PHE HIS GLN HIS PHE ASP LEU SEQRES 16 B 479 PRO ILE ASP ARG VAL LYS HIS THR VAL CYS PRO HIS TRP SEQRES 17 B 479 TYR ARG ALA PRO ALA GLY MET SER GLU ALA GLN PHE VAL SEQRES 18 B 479 ALA TYR CYS VAL GLU GLU LEU GLU LYS LEU ILE ALA ARG SEQRES 19 B 479 GLU GLY ALA ASP THR ILE ALA ALA PHE ILE ALA GLU PRO SEQRES 20 B 479 VAL MET GLY THR GLY GLY ILE ILE PRO PRO PRO GLN GLY SEQRES 21 B 479 TYR TRP GLU ALA ILE GLN ALA VAL LEU ARG LYS HIS ASP SEQRES 22 B 479 ILE LEU LEU ILE ALA ASP GLU VAL VAL CYS GLY PHE GLY SEQRES 23 B 479 ARG LEU GLY SER LYS MET GLY SER GLN HIS TYR GLY ILE SEQRES 24 B 479 LYS PRO ASP LEU ILE THR VAL ALA LYS GLY LEU THR SER SEQRES 25 B 479 ALA TYR ALA PRO LEU SER GLY VAL ILE VAL GLY GLU LYS SEQRES 26 B 479 VAL TRP ASP VAL ILE GLU LYS GLY SER GLN GLU HIS GLY SEQRES 27 B 479 PRO MET GLY HIS GLY TRP THR TYR SER GLY HIS PRO ILE SEQRES 28 B 479 CYS ALA ALA ALA ALA LEU ALA ASN LEU ASP ILE LEU GLU SEQRES 29 B 479 ARG GLU ASN LEU THR GLY ASN ALA ALA ASP VAL GLY ALA SEQRES 30 B 479 TYR LEU GLN GLN ARG LEU HIS GLU ALA PHE GLY ALA HIS SEQRES 31 B 479 PRO LEU VAL GLY GLU VAL ARG GLY VAL GLY MET LEU ALA SEQRES 32 B 479 ALA LEU GLU PHE MET ALA ASP LYS ASP ALA ARG THR PRO SEQRES 33 B 479 PHE ASP PRO ALA LEU LYS VAL GLY PRO LYS VAL SER ALA SEQRES 34 B 479 ALA ALA LEU GLU ASP GLY MET ILE ALA ARG ALA MET PRO SEQRES 35 B 479 HIS GLY ASP ILE LEU GLY PHE ALA PRO PRO LEU VAL THR SEQRES 36 B 479 THR ARG ALA GLU VAL ASP GLU ILE VAL GLY ILE ALA LYS SEQRES 37 B 479 GLN ALA VAL ASP GLU VAL ALA ASP GLU VAL LEU HET PLP A 500 15 HET PLP B 500 15 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 5 HOH *446(H2 O) HELIX 1 AA1 SER A 3 PHE A 15 1 13 HELIX 2 AA2 HIS A 21 SER A 27 1 7 HELIX 3 AA3 PHE A 55 CYS A 60 1 6 HELIX 4 AA4 ARG A 67 ALA A 82 1 16 HELIX 5 AA5 THR A 92 TRP A 106 1 15 HELIX 6 AA6 SER A 119 LEU A 138 1 20 HELIX 7 AA7 GLY A 157 THR A 164 1 8 HELIX 8 AA8 LEU A 166 HIS A 170 5 5 HELIX 9 AA9 HIS A 187 ALA A 191 5 5 HELIX 10 AB1 SER A 196 GLY A 216 1 21 HELIX 11 AB2 GLY A 240 HIS A 252 1 13 HELIX 12 AB3 MET A 272 GLY A 278 1 7 HELIX 13 AB4 ALA A 287 THR A 291 5 5 HELIX 14 AB5 GLU A 304 GLY A 318 1 15 HELIX 15 AB6 HIS A 329 GLU A 346 1 18 HELIX 16 AB7 ASN A 347 GLY A 368 1 22 HELIX 17 AB8 ASP A 398 LEU A 401 5 4 HELIX 18 AB9 LYS A 402 ASP A 414 1 13 HELIX 19 AC1 THR A 436 LEU A 459 1 24 HELIX 20 AC2 SER B 3 PHE B 15 1 13 HELIX 21 AC3 HIS B 21 SER B 27 1 7 HELIX 22 AC4 PHE B 55 CYS B 60 1 6 HELIX 23 AC5 ARG B 67 ALA B 82 1 16 HELIX 24 AC6 THR B 92 TRP B 106 1 15 HELIX 25 AC7 SER B 119 LEU B 138 1 20 HELIX 26 AC8 GLY B 157 THR B 164 1 8 HELIX 27 AC9 LEU B 166 HIS B 170 5 5 HELIX 28 AD1 HIS B 187 ALA B 191 5 5 HELIX 29 AD2 SER B 196 GLY B 216 1 21 HELIX 30 AD3 GLY B 240 HIS B 252 1 13 HELIX 31 AD4 MET B 272 GLY B 278 1 7 HELIX 32 AD5 ALA B 287 THR B 291 5 5 HELIX 33 AD6 GLU B 304 GLY B 318 1 15 HELIX 34 AD7 HIS B 329 GLU B 346 1 18 HELIX 35 AD8 ASN B 347 GLY B 368 1 22 HELIX 36 AD9 ASP B 398 LEU B 401 5 4 HELIX 37 AE1 LYS B 402 ASP B 414 1 13 HELIX 38 AE2 THR B 436 LEU B 459 1 24 SHEET 1 AA1 5 MET A 416 ILE A 417 0 SHEET 2 AA1 5 GLU A 50 ASP A 53 1 N ILE A 52 O ILE A 417 SHEET 3 AA1 5 ARG A 42 ASP A 45 -1 N ILE A 43 O TYR A 51 SHEET 4 AA1 5 ARG A 33 LYS A 39 -1 N GLY A 37 O GLU A 44 SHEET 5 AA1 5 HIS B 90 SER B 91 1 O SER B 91 N ARG A 33 SHEET 1 AA2 5 HIS A 90 SER A 91 0 SHEET 2 AA2 5 ARG B 33 LYS B 39 1 O ARG B 33 N SER A 91 SHEET 3 AA2 5 ARG B 42 ASP B 45 -1 O GLU B 44 N GLY B 37 SHEET 4 AA2 5 GLU B 50 ASP B 53 -1 O TYR B 51 N ILE B 43 SHEET 5 AA2 5 MET B 416 ILE B 417 1 O ILE B 417 N ILE B 52 SHEET 1 AA3 7 MET A 111 GLY A 117 0 SHEET 2 AA3 7 SER A 298 GLY A 303 -1 O VAL A 302 N LYS A 112 SHEET 3 AA3 7 LEU A 283 VAL A 286 -1 N ILE A 284 O ILE A 301 SHEET 4 AA3 7 LEU A 255 ASP A 259 1 N ALA A 258 O LEU A 283 SHEET 5 AA3 7 ILE A 220 ALA A 225 1 N PHE A 223 O ILE A 257 SHEET 6 AA3 7 LYS A 145 ARG A 149 1 N ILE A 147 O ALA A 222 SHEET 7 AA3 7 VAL A 180 THR A 183 1 O LYS A 181 N SER A 148 SHEET 1 AA4 4 VAL A 373 VAL A 379 0 SHEET 2 AA4 4 LEU A 382 PHE A 387 -1 O GLU A 386 N GLU A 375 SHEET 3 AA4 4 ILE A 426 PHE A 429 -1 O PHE A 429 N ALA A 383 SHEET 4 AA4 4 ARG A 419 ALA A 420 -1 N ARG A 419 O GLY A 428 SHEET 1 AA5 7 MET B 111 GLY B 117 0 SHEET 2 AA5 7 SER B 298 GLY B 303 -1 O VAL B 302 N LYS B 112 SHEET 3 AA5 7 LEU B 283 VAL B 286 -1 N ILE B 284 O ILE B 301 SHEET 4 AA5 7 LEU B 255 ASP B 259 1 N ALA B 258 O LEU B 283 SHEET 5 AA5 7 ILE B 220 ALA B 225 1 N PHE B 223 O ILE B 257 SHEET 6 AA5 7 LYS B 145 ARG B 149 1 N ILE B 147 O ALA B 222 SHEET 7 AA5 7 VAL B 180 THR B 183 1 O LYS B 181 N SER B 148 SHEET 1 AA6 4 VAL B 373 VAL B 379 0 SHEET 2 AA6 4 LEU B 382 PHE B 387 -1 O GLU B 386 N GLU B 375 SHEET 3 AA6 4 ILE B 426 PHE B 429 -1 O PHE B 429 N ALA B 383 SHEET 4 AA6 4 ARG B 419 ALA B 420 -1 N ARG B 419 O GLY B 428 CISPEP 1 LEU A 175 PRO A 176 0 1.95 CISPEP 2 LEU B 175 PRO B 176 0 1.77 SITE 1 AC1 15 SER A 119 GLY A 120 SER A 121 TYR A 153 SITE 2 AC1 15 HIS A 154 GLU A 226 ASP A 259 VAL A 261 SITE 3 AC1 15 VAL A 262 LYS A 288 HOH A 602 HOH A 609 SITE 4 AC1 15 HOH A 625 HOH A 800 THR B 325 SITE 1 AC2 15 TRP A 324 THR A 325 SER B 119 GLY B 120 SITE 2 AC2 15 SER B 121 TYR B 153 HIS B 154 GLU B 226 SITE 3 AC2 15 ASP B 259 VAL B 261 VAL B 262 LYS B 288 SITE 4 AC2 15 HOH B 602 HOH B 605 HOH B 659 CRYST1 63.523 122.162 64.296 90.00 116.46 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 0.015742 0.000000 0.007834 0.00000 SCALE2 0.000000 0.008186 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017373 0.00000