HEADER ISOMERASE 18-OCT-16 5M49 TITLE ALPHA-AMINO EPSILON-CAPROLACTAM RACEMASE IN COMPLEX WITH PLP AND D/L TITLE 2 ALPHA AMINO EPSILON-CAPROLACTAM (INTERNAL ALDIMINE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOTRANSFERASE CLASS-III; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHIZOBIUM FREIREI PRF 81; SOURCE 3 ORGANISM_TAXID: 363754; SOURCE 4 GENE: RHSP_08934; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PLP, RACEMASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.FRESE,P.W.SUTTON,J.P.TURKENBURG,G.GROGAN REVDAT 3 17-JAN-24 5M49 1 REMARK REVDAT 2 20-SEP-17 5M49 1 REMARK REVDAT 1 19-APR-17 5M49 0 JRNL AUTH A.FRESE,P.W.SUTTON,J.P.TURKENBURG,G.GROGAN JRNL TITL SNAPSHOTS OF THE CATALYTIC CYCLE OF THE INDUSTRIAL ENZYME JRNL TITL 2 ALPHA-AMINO-EPSILON-CAPROLACTAM RACEMASE (ACLR) OBSERVED JRNL TITL 3 USING X-RAY CRYSTALLOGRAPHY JRNL REF ACS CATALYSIS V. 7 1045 2017 JRNL REFN ESSN 2155-5435 JRNL DOI 10.1021/ACSCATAL.6B03056 REMARK 2 REMARK 2 RESOLUTION. 1.51 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.04 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 52841 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2767 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) : 1.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.55 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3902 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.1890 REMARK 3 BIN FREE R VALUE SET COUNT : 183 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3074 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 274 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : 0.49000 REMARK 3 B33 (A**2) : -0.20000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.18000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.073 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.076 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.218 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3182 ; 0.028 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3054 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4329 ; 2.538 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6991 ; 1.322 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 427 ; 6.284 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;31.489 ;22.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 467 ;12.611 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;22.889 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 495 ; 0.161 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3665 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 710 ; 0.006 ; 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): 1702 ; 1.902 ; 1.450 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1702 ; 1.902 ; 1.450 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2119 ; 2.519 ; 2.166 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2120 ; 2.518 ; 2.166 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1480 ; 2.620 ; 1.660 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1481 ; 2.619 ; 1.660 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2207 ; 3.754 ; 2.408 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3581 ; 4.845 ;18.637 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3582 ; 4.844 ;18.635 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 5M49 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200001908. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55609 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.510 REMARK 200 RESOLUTION RANGE LOW (A) : 45.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.02500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.51 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.05700 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: MOLREP REMARK 200 STARTING MODEL: 2ZUK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MGCL2, 25 % PEG 3350, 0.1 MM REMARK 280 HEPES (PH 7.0)., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 43.84800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.83950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 43.84800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 38.83950 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: 8780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 65.48559 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.14780 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 667 LIES ON A SPECIAL POSITION. 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 GLY A 98 REMARK 465 GLY A 149 REMARK 465 HIS A 150 REMARK 465 SER A 151 REMARK 465 VAL A 152 REMARK 465 GLN A 153 REMARK 465 ALA A 154 REMARK 465 ASP A 155 REMARK 465 ALA A 156 REMARK 465 ALA A 157 REMARK 465 SER A 423 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 GLN A 30 CD OE1 NE2 REMARK 470 ARG A 99 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 158 CE NZ REMARK 470 ASP A 160 CG OD1 OD2 REMARK 470 ARG A 222 NE CZ NH1 NH2 REMARK 470 GLU A 283 CG CD OE1 OE2 REMARK 470 GLU A 314 CD OE1 OE2 REMARK 470 ARG A 335 CZ NH1 NH2 REMARK 470 GLN A 362 CG CD OE1 NE2 REMARK 470 LYS A 373 CD CE NZ REMARK 470 MET A 390 CG SD CE REMARK 470 THR A 424 OG1 CG2 REMARK 470 VAL A 425 CG1 CG2 REMARK 470 SER A 426 OG REMARK 470 ASP A 427 CG OD1 OD2 REMARK 470 THR A 428 OG1 CG2 REMARK 470 LEU A 429 CG CD1 CD2 REMARK 470 SER A 431 OG REMARK 470 GLN A 432 CG CD OE1 NE2 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 A 614 O HOH A 804 1.93 REMARK 500 SG CYS A 353 O HOH A 678 1.94 REMARK 500 OE1 GLU A 365 O HOH A 601 2.07 REMARK 500 NH2 ARG A 359 O HOH A 602 2.08 REMARK 500 O HOH A 609 O HOH A 832 2.12 REMARK 500 OG SER A 66 O HOH A 603 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A 21 CG PHE A 21 CD1 -0.101 REMARK 500 SER A 95 CB SER A 95 OG 0.112 REMARK 500 SER A 148 CA SER A 148 CB -0.102 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 ASP A 9 CB - CG - OD2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG A 20 NE - CZ - NH2 ANGL. DEV. = 4.9 DEGREES REMARK 500 ARG A 33 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 33 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 GLU A 37 OE1 - CD - OE2 ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 TYR A 56 CB - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 GLU A 63 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASP A 112 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 119 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 324 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 324 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG A 359 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 359 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 368 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 368 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG A 409 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 409 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 TRP A 49 16.95 53.83 REMARK 500 ASN A 71 67.42 -150.82 REMARK 500 ALA A 75 12.50 -142.43 REMARK 500 SER A 209 -80.12 -75.59 REMARK 500 ALA A 245 -17.58 78.75 REMARK 500 LYS A 267 -105.54 42.40 REMARK 500 ALA A 367 69.45 -108.87 REMARK 500 GLU A 421 41.58 -90.11 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 A 874 DISTANCE = 6.33 ANGSTROMS 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 8F4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7F4 A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5M46 RELATED DB: PDB REMARK 900 5M46 IS THE ENZYME IN COMPLEX WITH ONLY PLP DBREF 5M49 A 1 436 UNP N6UXY4 N6UXY4_9RHIZ 1 436 SEQRES 1 A 436 MET ALA GLY ASN LEU TYR GLY ARG ASP GLY ALA ALA ILE SEQRES 2 A 436 GLY SER LEU GLN LYS LEU ARG PHE PHE PRO LEU ALA VAL SEQRES 3 A 436 ALA GLY GLY GLN GLY ALA ARG LEU VAL GLU GLU ASP GLY SEQRES 4 A 436 ARG GLU LEU ILE ASP LEU SER GLY ALA TRP GLY ALA ALA SEQRES 5 A 436 SER LEU GLY TYR GLY HIS PRO ALA ILE ILE GLU ALA VAL SEQRES 6 A 436 SER ARG ALA ALA ALA ASN PRO ALA GLY ALA SER ILE LEU SEQRES 7 A 436 SER ALA SER ASN ALA PRO ALA VAL ALA LEU ALA GLU ARG SEQRES 8 A 436 LEU THR ALA SER PHE PRO GLY ARG GLY THR HIS LYS VAL SEQRES 9 A 436 TRP PHE GLY HIS SER GLY SER ASP ALA ASN GLU ALA ALA SEQRES 10 A 436 TYR ARG ALA ILE THR ARG ALA THR GLY ARG THR GLY VAL SEQRES 11 A 436 ILE ALA PHE ILE GLY ALA TYR HIS GLY CYS THR VAL GLY SEQRES 12 A 436 SER MET ALA PHE SER GLY HIS SER VAL GLN ALA ASP ALA SEQRES 13 A 436 ALA LYS ALA ASP GLY LEU ILE LEU LEU PRO TYR PRO ASP SEQRES 14 A 436 PRO TYR ARG PRO TYR GLN ASP ASP PRO THR GLY ASP ALA SEQRES 15 A 436 VAL LEU ALA LEU LEU LYS GLU ARG LEU ALA ALA VAL PRO SEQRES 16 A 436 ALA GLY SER ILE ALA ALA ALA PHE ILE GLU PRO ILE GLN SEQRES 17 A 436 SER ASP GLY GLY LEU ILE VAL PRO PRO ASP GLY PHE LEU SEQRES 18 A 436 ARG LYS PHE ALA ASP ILE CYS ARG ALA HIS GLY ILE SER SEQRES 19 A 436 VAL VAL CYS ASP GLU VAL LYS VAL GLY LEU ALA ARG SER SEQRES 20 A 436 GLY ARG LEU HIS CYS PHE GLU HIS GLU GLY PHE VAL PRO SEQRES 21 A 436 ASP ILE LEU VAL LEU GLY LYS GLY LEU GLY GLY GLY LEU SEQRES 22 A 436 PRO LEU SER ALA VAL ILE ALA PRO ALA GLU ILE LEU ASP SEQRES 23 A 436 CYS ALA SER ALA PHE ALA MET GLN THR LEU HIS GLY ASN SEQRES 24 A 436 PRO VAL CYS ALA ALA ALA GLY LEU ALA VAL LEU GLU THR SEQRES 25 A 436 ILE GLU ALA GLU ASN LEU THR THR ALA ALA GLU ARG LYS SEQRES 26 A 436 GLY LYS LEU LEU ARG GLU GLY LEU ALA ARG LEU ALA GLU SEQRES 27 A 436 ARG HIS GLU LEU ILE GLY ASP ILE ARG GLY ARG GLY LEU SEQRES 28 A 436 ALA CYS GLY VAL GLU LEU VAL ARG ASN ARG GLN SER ARG SEQRES 29 A 436 GLU PRO ALA ARG ALA GLU THR ALA LYS LEU ILE TYR ARG SEQRES 30 A 436 ALA TYR GLU LEU GLY LEU VAL LEU TYR TYR VAL GLY MET SEQRES 31 A 436 ASN GLY ASN VAL LEU GLU MET THR PRO PRO LEU THR MET SEQRES 32 A 436 THR GLU ASP GLU VAL ARG HIS ALA VAL ASN LEU LEU ASP SEQRES 33 A 436 GLN ALA PHE THR GLU LEU SER THR VAL SER ASP THR LEU SEQRES 34 A 436 VAL SER GLN PHE ALA GLY TRP HET PLP A 501 15 HET 8F4 A 502 9 HET 7F4 A 503 9 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM 8F4 (3~{S})-3-AZANYLAZEPAN-2-ONE HETNAM 7F4 (3~{R})-3-AZANYLAZEPAN-2-ONE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 8F4 C6 H12 N2 O FORMUL 4 7F4 C6 H12 N2 O FORMUL 5 HOH *274(H2 O) HELIX 1 AA1 ASN A 4 ILE A 13 1 10 HELIX 2 AA2 GLY A 14 LYS A 18 5 5 HELIX 3 AA3 GLY A 47 ALA A 51 5 5 HELIX 4 AA4 HIS A 58 ASN A 71 1 14 HELIX 5 AA5 ASN A 82 SER A 95 1 14 HELIX 6 AA6 SER A 109 GLY A 126 1 18 HELIX 7 AA7 THR A 141 ALA A 146 1 6 HELIX 8 AA8 PRO A 173 ASP A 177 5 5 HELIX 9 AA9 GLY A 180 ALA A 193 1 14 HELIX 10 AB1 GLY A 219 HIS A 231 1 13 HELIX 11 AB2 HIS A 251 GLU A 256 5 6 HELIX 12 AB3 GLY A 266 GLY A 271 5 6 HELIX 13 AB4 ALA A 282 ASP A 286 1 5 HELIX 14 AB5 ASN A 299 GLU A 316 1 18 HELIX 15 AB6 ASN A 317 HIS A 340 1 24 HELIX 16 AB7 ALA A 367 GLY A 382 1 16 HELIX 17 AB8 THR A 404 GLU A 421 1 18 HELIX 18 AB9 SER A 426 GLN A 432 1 7 SHEET 1 AA1 4 VAL A 26 GLN A 30 0 SHEET 2 AA1 4 ARG A 33 GLU A 36 -1 O VAL A 35 N ALA A 27 SHEET 3 AA1 4 GLU A 41 ASP A 44 -1 O LEU A 42 N LEU A 34 SHEET 4 AA1 4 LEU A 383 VAL A 384 1 O VAL A 384 N ILE A 43 SHEET 1 AA2 7 HIS A 102 GLY A 107 0 SHEET 2 AA2 7 SER A 276 PRO A 281 -1 O ALA A 280 N LYS A 103 SHEET 3 AA2 7 ILE A 262 LEU A 265 -1 N LEU A 265 O ALA A 277 SHEET 4 AA2 7 SER A 234 ASP A 238 1 N CYS A 237 O ILE A 262 SHEET 5 AA2 7 ILE A 199 ILE A 204 1 N ALA A 202 O VAL A 236 SHEET 6 AA2 7 GLY A 129 PHE A 133 1 N ILE A 131 O PHE A 203 SHEET 7 AA2 7 LEU A 162 LEU A 165 1 O ILE A 163 N VAL A 130 SHEET 1 AA3 4 ILE A 343 ARG A 349 0 SHEET 2 AA3 4 ALA A 352 LEU A 357 -1 O GLU A 356 N GLY A 344 SHEET 3 AA3 4 VAL A 394 MET A 397 -1 O LEU A 395 N VAL A 355 SHEET 4 AA3 4 TYR A 386 VAL A 388 -1 N TYR A 386 O GLU A 396 LINK NZ LYS A 267 C4A PLP A 501 1555 1555 1.43 SITE 1 AC1 16 SER A 109 GLY A 110 SER A 111 TYR A 137 SITE 2 AC1 16 HIS A 138 GLU A 205 ASP A 238 VAL A 240 SITE 3 AC1 16 LYS A 241 LYS A 267 GLN A 294 THR A 295 SITE 4 AC1 16 HOH A 619 HOH A 632 HOH A 664 HOH A 723 SITE 1 AC2 11 LEU A 19 TRP A 49 TYR A 137 ASP A 210 SITE 2 AC2 11 LYS A 241 LYS A 267 THR A 295 TRP A 436 SITE 3 AC2 11 7F4 A 503 HOH A 635 HOH A 723 SITE 1 AC3 10 TRP A 49 TYR A 137 ASP A 210 LYS A 241 SITE 2 AC3 10 LYS A 267 THR A 295 TRP A 436 8F4 A 502 SITE 3 AC3 10 HOH A 635 HOH A 723 CRYST1 87.696 77.679 57.602 90.00 112.68 90.00 C 1 2 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 0.011403 0.000000 0.004764 0.00000 SCALE2 0.000000 0.012873 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018815 0.00000