HEADER TRANSFERASE 06-JUL-16 5KR4 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 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: 562 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 5KR4 1 REMARK REVDAT 2 30-JAN-19 5KR4 1 JRNL REVDAT 1 12-JUL-17 5KR4 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. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 66296 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3542 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4724 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.21 REMARK 3 BIN R VALUE (WORKING SET) : 0.2610 REMARK 3 BIN FREE R VALUE SET COUNT : 259 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6974 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 447 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -1.26000 REMARK 3 B33 (A**2) : 1.28000 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): 0.178 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.544 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7229 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6836 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9818 ; 1.565 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15733 ; 0.979 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 922 ; 6.109 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 313 ;32.161 ;23.866 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1143 ;13.551 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;15.258 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1062 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8276 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1634 ; 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): 3679 ; 1.318 ; 1.976 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3678 ; 1.318 ; 1.975 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4604 ; 1.960 ; 2.958 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4605 ; 1.960 ; 2.959 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3550 ; 2.057 ; 2.204 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3550 ; 2.057 ; 2.204 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5215 ; 3.208 ; 3.220 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 31345 ; 4.641 ;37.840 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 31346 ; 4.641 ;37.840 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 3 459 B 3 459 30012 0.05 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 5KR4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222639. 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 : 70329 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 45.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.15600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.72600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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 (%): 50.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 150 PLUS 150 NL DROPS WITH PROTEIN AT REMARK 280 10 MG/ML AND RESERVOIR CONDITIONS OF 12% PEG 8000, 15% GLYCEROL, REMARK 280 150 MM MGCL2, 100 MM TRIS PH 7.1. MICROSEEDS WERE USED FOR REMARK 280 NUCLEATION OF THE CRYSTALS., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 33.52650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.81450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 60.89150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.81450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.52650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 60.89150 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: 12390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 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 HIS A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 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 465 THR B 2 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 O HOH B 771 O HOH B 791 2.02 REMARK 500 O1P PLP A 501 O HOH A 601 2.07 REMARK 500 O HOH B 791 O HOH B 828 2.10 REMARK 500 O HOH B 636 O HOH B 809 2.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLN A 239 OE1 GLU B 442 3654 1.77 REMARK 500 NE2 GLN A 239 OE2 GLU B 442 3654 2.09 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 267 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 267 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 345 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 LYS B 143 CD - CE - NZ ANGL. DEV. = 14.1 DEGREES REMARK 500 ARG B 267 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 267 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG B 345 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 345 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 362 NE - CZ - NH2 ANGL. DEV. = -3.1 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 62.69 38.52 REMARK 500 HIS A 21 109.15 -51.19 REMARK 500 LEU A 81 97.13 -165.97 REMARK 500 LYS A 112 -53.32 -127.02 REMARK 500 SER A 148 -164.37 -119.29 REMARK 500 ARG A 151 -0.50 72.55 REMARK 500 THR A 183 -169.22 -103.62 REMARK 500 PHE A 265 47.22 71.80 REMARK 500 ALA A 287 -150.46 -169.59 REMARK 500 LYS A 288 -94.04 42.98 REMARK 500 MET A 381 30.14 -94.80 REMARK 500 SER B 19 62.04 37.53 REMARK 500 HIS B 21 107.39 -50.26 REMARK 500 LEU B 81 98.81 -165.38 REMARK 500 LYS B 112 -55.11 -126.30 REMARK 500 SER B 148 -165.42 -118.71 REMARK 500 ARG B 151 -0.98 72.48 REMARK 500 THR B 183 -168.63 -103.73 REMARK 500 PHE B 265 46.06 70.84 REMARK 500 ALA B 287 -146.45 -168.75 REMARK 500 LYS B 288 -96.14 43.04 REMARK 500 REMARK 500 REMARK: NULL 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 501 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 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: 5KQW RELATED DB: PDB REMARK 900 RELATED ID: 5KR3 RELATED DB: PDB REMARK 900 RELATED ID: 5KR5 RELATED DB: PDB REMARK 900 RELATED ID: 5KR6 RELATED DB: PDB DBREF 5KR4 A -19 459 PDB 5KR4 5KR4 -19 459 DBREF 5KR4 B -19 459 PDB 5KR4 5KR4 -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 THR SER LEU ASP GLN SEQRES 3 A 479 LEU PHE GLU GLU 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 LYS ILE VAL THR GLY GLY LYS GLY ILE ARG ILE GLU ASP SEQRES 6 A 479 HIS GLN 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 ILE 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 LYS 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 ALA 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 SER ASP GLU VAL VAL CYS GLY PHE GLY SEQRES 23 A 479 ARG LEU GLY SER LYS MET GLY ALA 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 VAL 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 VAL 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 THR SER LEU ASP GLN SEQRES 3 B 479 LEU PHE GLU GLU 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 LYS ILE VAL THR GLY GLY LYS GLY ILE ARG ILE GLU ASP SEQRES 6 B 479 HIS GLN 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 ILE 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 LYS 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 ALA 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 SER ASP GLU VAL VAL CYS GLY PHE GLY SEQRES 23 B 479 ARG LEU GLY SER LYS MET GLY ALA 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 VAL 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 VAL LYS SEQRES 37 B 479 GLN ALA VAL ASP GLU VAL ALA ASP GLU VAL LEU HET PLP A 501 15 HET EDO A 502 4 HET EDO A 503 4 HET EDO A 504 4 HET PLP B 500 15 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 4 EDO 3(C2 H6 O2) FORMUL 8 HOH *447(H2 O) HELIX 1 AA1 SER A 3 HIS A 14 1 12 HELIX 2 AA2 HIS A 21 GLY A 28 1 8 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 ILE A 158 THR A 164 1 7 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 ASP A 253 1 14 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 LEU B 4 PHE B 15 1 12 HELIX 21 AC3 HIS B 21 GLY B 28 1 8 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 ILE B 158 THR B 164 1 7 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 ASP B 253 1 14 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 8 PHE A 15 MET A 16 0 SHEET 2 AA1 8 MET B 111 GLY B 117 1 O VAL B 114 N MET A 16 SHEET 3 AA1 8 SER B 298 GLY B 303 -1 O VAL B 302 N LYS B 113 SHEET 4 AA1 8 LEU B 283 VAL B 286 -1 N ILE B 284 O ILE B 301 SHEET 5 AA1 8 LEU B 255 ASP B 259 1 N SER B 258 O LEU B 283 SHEET 6 AA1 8 ILE B 220 ALA B 225 1 N ALA B 225 O ASP B 259 SHEET 7 AA1 8 LYS B 145 ARG B 149 1 N ILE B 147 O ALA B 222 SHEET 8 AA1 8 VAL B 180 THR B 183 1 O LYS B 181 N SER B 148 SHEET 1 AA2 5 VAL A 416 ILE A 417 0 SHEET 2 AA2 5 GLU A 50 ASP A 53 1 N ILE A 52 O ILE A 417 SHEET 3 AA2 5 ARG A 42 ASP A 45 -1 N ILE A 43 O TYR A 51 SHEET 4 AA2 5 LYS A 33 LYS A 39 -1 N LYS A 39 O ARG A 42 SHEET 5 AA2 5 HIS B 90 SER B 91 1 O SER B 91 N VAL A 35 SHEET 1 AA3 5 HIS A 90 SER A 91 0 SHEET 2 AA3 5 LYS B 33 LYS B 39 1 O VAL B 35 N SER A 91 SHEET 3 AA3 5 ARG B 42 ASP B 45 -1 O GLU B 44 N GLY B 37 SHEET 4 AA3 5 GLU B 50 ASP B 53 -1 O TYR B 51 N ILE B 43 SHEET 5 AA3 5 VAL B 416 ILE B 417 1 O ILE B 417 N ILE B 52 SHEET 1 AA4 7 MET A 111 GLY A 117 0 SHEET 2 AA4 7 SER A 298 GLY A 303 -1 O VAL A 302 N LYS A 113 SHEET 3 AA4 7 LEU A 283 VAL A 286 -1 N ILE A 284 O ILE A 301 SHEET 4 AA4 7 LEU A 255 ASP A 259 1 N SER A 258 O LEU A 283 SHEET 5 AA4 7 ILE A 220 ALA A 225 1 N PHE A 223 O ILE A 257 SHEET 6 AA4 7 LYS A 145 ARG A 149 1 N ILE A 147 O ALA A 222 SHEET 7 AA4 7 VAL A 180 THR A 183 1 O LYS A 181 N SER A 148 SHEET 1 AA5 4 VAL A 373 VAL A 379 0 SHEET 2 AA5 4 LEU A 382 PHE A 387 -1 O ALA A 384 N ARG A 377 SHEET 3 AA5 4 ILE A 426 PHE A 429 -1 O PHE A 429 N ALA A 383 SHEET 4 AA5 4 ARG A 419 MET A 421 -1 N ARG A 419 O GLY A 428 SHEET 1 AA6 4 VAL B 373 VAL B 379 0 SHEET 2 AA6 4 LEU B 382 PHE B 387 -1 O ALA B 384 N ARG B 377 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 4.74 CISPEP 2 LEU B 175 PRO B 176 0 6.31 SITE 1 AC1 16 SER A 119 GLY A 120 SER A 121 TYR A 153 SITE 2 AC1 16 HIS A 154 GLU A 226 ASP A 259 VAL A 261 SITE 3 AC1 16 VAL A 262 LYS A 288 EDO A 503 HOH A 601 SITE 4 AC1 16 HOH A 616 HOH A 624 HOH A 679 THR B 325 SITE 1 AC2 4 GLY A 110 ASP A 282 GLU A 304 LYS A 305 SITE 1 AC3 7 THR A 231 LYS A 288 ARG A 419 PLP A 501 SITE 2 AC3 7 HOH A 646 TYR B 87 THR B 325 SITE 1 AC4 4 GLU A 150 GLY A 165 HIS A 170 HIS A 182 SITE 1 AC5 17 TRP A 324 THR A 325 HOH A 692 SER B 119 SITE 2 AC5 17 GLY B 120 SER B 121 TYR B 153 HIS B 154 SITE 3 AC5 17 GLU B 226 ASP B 259 VAL B 261 VAL B 262 SITE 4 AC5 17 LYS B 288 HOH B 601 HOH B 602 HOH B 612 SITE 5 AC5 17 HOH B 679 CRYST1 67.053 121.783 125.629 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 0.014914 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008211 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007960 0.00000