HEADER LYASE 17-OCT-16 5M3Z TITLE CRYSTAL STRUCTURE OF CITROBACTER FREUNDII METHIONINE GAMMA-LYASE WITH TITLE 2 C115H REPLACEMENT IN THE COMPLEX WITH L-NORLEUCINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONINE GAMMA-LYASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.4.1.11; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CITROBACTER FREUNDII; SOURCE 3 ORGANISM_TAXID: 546; SOURCE 4 GENE: AN672_11005, HMPREF3212_02785, TN42_08855, TO64_18625; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS METHIONINE GAMMA-LYASE, C115H SUBSTITUTION, L-NORLEUCINE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.V.REVTOVICH,A.D.NIKULIN,N.V.ANUFRIEVA,E.A.MOROZOVA,T.V.DEMIDKINA REVDAT 3 17-JAN-24 5M3Z 1 REMARK REVDAT 2 05-JUL-17 5M3Z 1 JRNL REVDAT 1 28-JUN-17 5M3Z 0 JRNL AUTH S.V.REVTOVICH,E.A.MOROZOVA,V.V.KULIKOVA,N.V.ANUFRIEVA, JRNL AUTH 2 T.I.OSIPOVA,V.S.KOVAL,A.D.NIKULIN,T.V.DEMIDKINA JRNL TITL CRYSTAL STRUCTURE OF MUTANT FORM CYS115HIS OF CITROBACTER JRNL TITL 2 FREUNDII METHIONINE GAMMA-LYASE COMPLEXED WITH L-NORLEUCINE. JRNL REF BIOCHIM. BIOPHYS. ACTA V.1865 1123 2017 JRNL REFN ISSN 0006-3002 JRNL PMID 28602917 JRNL DOI 10.1016/J.BBAPAP.2017.06.001 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 88.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 74318 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) : 0.130 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3806 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5339 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 267 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2992 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 58 REMARK 3 SOLVENT ATOMS : 346 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : 0.71000 REMARK 3 B33 (A**2) : -0.92000 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): 0.054 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.054 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.109 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3237 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3117 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4415 ; 1.833 ; 1.984 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7181 ; 1.255 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 429 ; 6.327 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;39.801 ;24.328 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 537 ;13.300 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.755 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 508 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3686 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 707 ; 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): 1632 ; 4.298 ; 2.332 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1631 ; 4.248 ; 2.330 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2044 ; 4.966 ; 3.502 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2045 ; 4.970 ; 3.503 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1604 ; 5.780 ; 2.759 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1605 ; 5.779 ; 2.759 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2356 ; 6.997 ; 3.992 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3960 ; 6.451 ;20.734 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3751 ; 6.375 ;19.960 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6352 ; 6.045 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 71 ;29.771 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6554 ;20.356 ; 5.000 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 5M3Z 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_1200001894. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-16 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 : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78132 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 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: PHASER REMARK 200 STARTING MODEL: 2RFV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MGL 20MG/ML, PEG MME 2000 37.5%, 50 ML REMARK 280 TRISHCL, 25MM DTT, 0.2 MM PLP, PH 8.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 28.25650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 61.50950 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 63.78850 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.25650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 61.50950 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 63.78850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.25650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 61.50950 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 63.78850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.25650 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 61.50950 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 63.78850 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 23590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -102.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 127.57700 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 127.57700 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 504 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 664 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 726 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 750 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 795 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 SER A 2 REMARK 465 PHE A 398 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 525 O HOH A 696 2.16 REMARK 500 O HOH A 652 O HOH A 773 2.19 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 GLU A 344 CD GLU A 344 OE1 0.075 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 78 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 256 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 256 NE - CZ - NH2 ANGL. DEV. = -4.3 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 ILE A 57 -51.07 -131.83 REMARK 500 SER A 190 162.68 69.09 REMARK 500 LYS A 210 -126.67 -87.75 REMARK 500 LYS A 210 -121.34 -93.47 REMARK 500 VAL A 236 -56.17 -121.36 REMARK 500 SER A 339 172.65 68.79 REMARK 500 MET A 353 -79.78 -102.69 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 845 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH A 846 DISTANCE = 6.45 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NLE A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PY6 A 404 DBREF1 5M3Z A 1 398 UNP A0A0A5P8W7_CITFR DBREF2 5M3Z A A0A0A5P8W7 1 398 SEQADV 5M3Z HIS A 115 UNP A0A0A5P8W CYS 115 ENGINEERED MUTATION SEQRES 1 A 398 MET SER ASP CSO ARG THR TYR GLY PHE ASN THR GLN ILE SEQRES 2 A 398 VAL HIS ALA GLY GLN GLN PRO ASP PRO SER THR GLY ALA SEQRES 3 A 398 LEU SER THR PRO ILE PHE GLN THR SER THR PHE VAL PHE SEQRES 4 A 398 ASP SER ALA GLU GLN GLY ALA ALA ARG PHE ALA LEU GLU SEQRES 5 A 398 GLU SER GLY TYR ILE TYR THR ARG LEU GLY ASN PRO THR SEQRES 6 A 398 THR ASP ALA LEU GLU LYS LYS LEU ALA VAL LEU GLU ARG SEQRES 7 A 398 GLY GLU ALA GLY LEU ALA THR ALA SER GLY ILE SER ALA SEQRES 8 A 398 ILE THR THR THR LEU LEU THR LEU CYS GLN GLN GLY ASP SEQRES 9 A 398 HIS ILE VAL SER ALA SER ALA ILE TYR GLY HIS THR HIS SEQRES 10 A 398 ALA PHE LEU SER HIS SER MET PRO LYS PHE GLY ILE ASN SEQRES 11 A 398 VAL SER PHE VAL ASP ALA ALA LYS PRO GLU GLU ILE ARG SEQRES 12 A 398 ALA ALA MET ARG PRO GLU THR LYS VAL VAL TYR ILE GLU SEQRES 13 A 398 THR PRO ALA ASN PRO THR LEU SER LEU VAL ASP ILE GLU SEQRES 14 A 398 THR VAL ALA GLY ILE ALA HIS GLN GLN GLY ALA LEU LEU SEQRES 15 A 398 VAL VAL ASP ASN THR PHE MET SER PRO TYR CYS GLN GLN SEQRES 16 A 398 PRO LEU GLN LEU GLY ALA ASP ILE VAL VAL HIS SER VAL SEQRES 17 A 398 THR LYS TYR ILE ASN GLY HIS GLY ASP VAL ILE GLY GLY SEQRES 18 A 398 ILE ILE VAL GLY LYS GLN GLU PHE ILE ASP GLN ALA ARG SEQRES 19 A 398 PHE VAL GLY LEU LYS ASP ILE THR GLY GLY CYS MET SER SEQRES 20 A 398 PRO PHE ASN ALA TRP LEU THR LEU ARG GLY VAL LYS THR SEQRES 21 A 398 LEU GLY ILE ARG MET GLU ARG HIS CYS GLU ASN ALA LEU SEQRES 22 A 398 LYS ILE ALA ARG PHE LEU GLU GLY HIS PRO SER ILE THR SEQRES 23 A 398 ARG VAL TYR TYR PRO GLY LEU SER SER HIS PRO GLN TYR SEQRES 24 A 398 GLU LEU GLY GLN ARG GLN MET SER LEU PRO GLY GLY ILE SEQRES 25 A 398 ILE SER PHE GLU ILE ALA GLY GLY LEU GLU ALA GLY ARG SEQRES 26 A 398 ARG MET ILE ASN SER VAL GLU LEU CYS LEU LEU ALA VAL SEQRES 27 A 398 SER LEU GLY ASP THR GLU THR LEU ILE GLN HIS PRO ALA SEQRES 28 A 398 SER MET THR HIS SER PRO VAL ALA PRO GLU GLU ARG LEU SEQRES 29 A 398 LYS ALA GLY ILE THR ASP GLY LEU ILE ARG LEU SER VAL SEQRES 30 A 398 GLY LEU GLU ASP PRO GLU ASP ILE ILE ASN ASP LEU GLU SEQRES 31 A 398 HIS ALA ILE ARG LYS ALA THR PHE MODRES 5M3Z CSO A 4 CYS MODIFIED RESIDUE HET CSO A 4 7 HET PLP A 401 15 HET NLE A 402 9 HET PGE A 403 10 HET PY6 A 404 24 HETNAM CSO S-HYDROXYCYSTEINE HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM NLE NORLEUCINE HETNAM PGE TRIETHYLENE GLYCOL HETNAM PY6 2-[O-PHOSPHONOPYRIDOXYL]-AMINO-HEXANOIC ACID HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN PY6 VITAMIN B6 COMPLEXED WITH 2-AMINO-HEXANOIC ACID FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 NLE C6 H13 N O2 FORMUL 4 PGE C6 H14 O4 FORMUL 5 PY6 C14 H23 N2 O7 P FORMUL 6 HOH *346(H2 O) HELIX 1 AA1 ASP A 3 TYR A 7 5 5 HELIX 2 AA2 GLY A 8 ALA A 16 1 9 HELIX 3 AA3 SER A 41 ALA A 50 1 10 HELIX 4 AA4 ASN A 63 ARG A 78 1 16 HELIX 5 AA5 SER A 87 CYS A 100 1 14 HELIX 6 AA6 TYR A 113 PHE A 127 1 15 HELIX 7 AA7 LYS A 138 MET A 146 1 9 HELIX 8 AA8 ASP A 167 GLN A 178 1 12 HELIX 9 AA9 GLN A 195 GLY A 200 5 6 HELIX 10 AB1 LYS A 226 VAL A 236 1 11 HELIX 11 AB2 VAL A 236 ILE A 241 1 6 HELIX 12 AB3 SER A 247 LYS A 259 1 13 HELIX 13 AB4 THR A 260 GLY A 281 1 22 HELIX 14 AB5 GLN A 298 MET A 306 1 9 HELIX 15 AB6 GLY A 319 ASN A 329 1 11 HELIX 16 AB7 ALA A 359 ALA A 366 1 8 HELIX 17 AB8 ASP A 381 THR A 397 1 17 SHEET 1 AA1 7 ALA A 81 THR A 85 0 SHEET 2 AA1 7 GLY A 221 GLY A 225 -1 O GLY A 221 N THR A 85 SHEET 3 AA1 7 ILE A 203 SER A 207 -1 N VAL A 204 O VAL A 224 SHEET 4 AA1 7 LEU A 181 ASP A 185 1 N VAL A 184 O ILE A 203 SHEET 5 AA1 7 THR A 150 GLU A 156 1 N VAL A 153 O VAL A 183 SHEET 6 AA1 7 HIS A 105 ALA A 109 1 N HIS A 105 O LYS A 151 SHEET 7 AA1 7 ASN A 130 VAL A 134 1 O SER A 132 N SER A 108 SHEET 1 AA2 5 ILE A 285 TYR A 289 0 SHEET 2 AA2 5 ILE A 312 ILE A 317 -1 O SER A 314 N TYR A 289 SHEET 3 AA2 5 LEU A 372 SER A 376 -1 O LEU A 375 N ILE A 313 SHEET 4 AA2 5 LEU A 346 GLN A 348 -1 N LEU A 346 O SER A 376 SHEET 5 AA2 5 LEU A 335 LEU A 336 1 N LEU A 335 O ILE A 347 LINK C ASP A 3 N CSO A 4 1555 1555 1.30 LINK C CSO A 4 N ARG A 5 1555 1555 1.35 LINK NZ BLYS A 210 C4ABPLP A 401 1555 1555 1.47 CISPEP 1 THR A 157 PRO A 158 0 -9.65 CISPEP 2 ASN A 160 PRO A 161 0 -3.83 SITE 1 AC1 15 TYR A 58 ARG A 60 SER A 87 GLY A 88 SITE 2 AC1 15 ILE A 89 TYR A 113 GLU A 156 ASP A 185 SITE 3 AC1 15 PHE A 188 SER A 207 THR A 209 LYS A 210 SITE 4 AC1 15 GLY A 220 NLE A 402 PY6 A 404 SITE 1 AC2 10 PHE A 49 TYR A 58 TYR A 113 LYS A 210 SITE 2 AC2 10 VAL A 338 SER A 339 ARG A 374 PLP A 401 SITE 3 AC2 10 PY6 A 404 HOH A 501 SITE 1 AC3 8 PRO A 191 TYR A 192 CYS A 193 GLN A 194 SITE 2 AC3 8 GLN A 195 SER A 307 HOH A 617 HOH A 694 SITE 1 AC4 19 TYR A 58 ARG A 60 SER A 87 GLY A 88 SITE 2 AC4 19 ILE A 89 TYR A 113 ASP A 185 THR A 187 SITE 3 AC4 19 SER A 207 THR A 209 LYS A 210 GLY A 220 SITE 4 AC4 19 VAL A 338 SER A 339 ARG A 374 PLP A 401 SITE 5 AC4 19 NLE A 402 HOH A 501 HOH A 530 CRYST1 56.513 123.019 127.577 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017695 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008129 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007838 0.00000