HEADER LYASE 28-JAN-13 4IXS TITLE NATIVE STRUCTURE OF XOMETC AT PH 5.2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTATHIONINE GAMMA-LYASE-LIKE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 EC: 4.4.1.1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS ORYZAE PV. ORYZAE; SOURCE 3 ORGANISM_TAXID: 291331; SOURCE 4 STRAIN: KACC 10331/KXO85; SOURCE 5 GENE: METB, XOO0778; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PLP DEPENDENT ENZYME, LYASE, XOMETC, CYS-MET METABOLISM PLP DEPENDENT KEYWDS 2 ENZYME, CYSTATHIONINE GAMMA/BETA LYASE, PLP BINDING EXPDTA X-RAY DIFFRACTION AUTHOR H.P.T.NGO,J.K.KIM,L.W.KANG REVDAT 5 06-DEC-23 4IXS 1 REMARK REVDAT 4 20-SEP-23 4IXS 1 REMARK LINK REVDAT 3 03-MAY-17 4IXS 1 REMARK HET HETATM REVDAT 2 26-FEB-14 4IXS 1 JRNL REVDAT 1 29-JAN-14 4IXS 0 SPRSDE 29-JAN-14 4IXS 3NNP JRNL AUTH H.P.NGO,N.M.CERQUEIRA,J.K.KIM,M.K.HONG,P.A.FERNANDES, JRNL AUTH 2 M.J.RAMOS,L.W.KANG JRNL TITL PLP UNDERGOES CONFORMATIONAL CHANGES DURING THE COURSE OF AN JRNL TITL 2 ENZYMATIC REACTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 596 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24531493 JRNL DOI 10.1107/S1399004713031283 REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 33405 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1762 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) : 2.29 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.35 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2354 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 116 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5526 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 273 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.01000 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): 0.321 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.241 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.161 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.597 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5661 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7679 ; 1.992 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 730 ; 7.074 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 224 ;36.440 ;22.946 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 906 ;20.491 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 43 ;22.879 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 892 ; 0.154 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4235 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3639 ; 1.009 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5806 ; 1.817 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2022 ; 3.150 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1870 ; 4.926 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.40 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 4IXS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000077343. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35240 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASES REMARK 200 STARTING MODEL: PDB ENTRY 3E6G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG 3350, 0.2M LITHIUM SULFATE, REMARK 280 0.1M BIS-TRIS, 0.2M SODIUM THIOCYANATE, PH 5.2, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 73.08200 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 73.08200 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 42.86100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.17850 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.86100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.17850 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 73.08200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.86100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 62.17850 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 73.08200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.86100 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 62.17850 REMARK 290 SMTRY3 8 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 18450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -109.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 85.72200 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 73.08200 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 ASN A 3 REMARK 465 ARG A 4 REMARK 465 THR A 5 REMARK 465 THR A 6 REMARK 465 HIS A 7 REMARK 465 SER A 8 REMARK 465 HIS A 9 REMARK 465 ASP A 10 REMARK 465 GLY A 11 REMARK 465 ASP A 12 REMARK 465 ARG A 13 REMARK 465 SER A 48 REMARK 465 SER A 49 REMARK 465 PRO A 50 REMARK 465 GLY A 51 REMARK 465 GLU A 52 REMARK 465 HIS A 53 REMARK 465 GLN A 54 REMARK 465 GLY A 55 REMARK 465 PHE A 56 REMARK 465 GLU A 57 REMARK 465 TYR A 58 REMARK 465 HIS A 355 REMARK 465 ALA A 356 REMARK 465 SER A 357 REMARK 465 ILE A 358 REMARK 465 PRO A 359 REMARK 465 VAL A 360 REMARK 465 ALA A 361 REMARK 465 ARG A 362 REMARK 465 ARG A 363 REMARK 465 ASN A 395 REMARK 465 GLN A 396 REMARK 465 ASN A 397 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 ASN B 3 REMARK 465 ARG B 4 REMARK 465 THR B 5 REMARK 465 THR B 6 REMARK 465 HIS B 7 REMARK 465 SER B 8 REMARK 465 HIS B 9 REMARK 465 ASP B 10 REMARK 465 GLY B 11 REMARK 465 ASP B 12 REMARK 465 ARG B 13 REMARK 465 ALA B 14 REMARK 465 GLY B 51 REMARK 465 GLU B 52 REMARK 465 HIS B 53 REMARK 465 GLN B 54 REMARK 465 GLY B 55 REMARK 465 PHE B 56 REMARK 465 GLU B 57 REMARK 465 TYR B 58 REMARK 465 ASN B 395 REMARK 465 GLN B 396 REMARK 465 ASN B 397 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 PRO B 350 O THR B 354 2.01 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 390 CG GLU A 390 CD 0.093 REMARK 500 VAL B 205 CB VAL B 205 CG1 -0.139 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 MET A 235 CG - SD - CE ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG B 66 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG B 66 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 VAL B 153 CB - CA - C ANGL. DEV. = -13.8 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 ARG A 60 -58.57 70.54 REMARK 500 ASP A 110 40.24 -78.82 REMARK 500 VAL A 122 -60.68 -122.94 REMARK 500 ASP A 135 87.80 -66.38 REMARK 500 SER A 190 162.09 69.49 REMARK 500 LLP A 210 -109.82 -93.68 REMARK 500 ASN A 228 85.38 -151.63 REMARK 500 MET A 353 -113.45 -87.31 REMARK 500 ASN B 63 111.63 -161.09 REMARK 500 ASP B 135 86.22 -68.68 REMARK 500 SER B 190 161.98 78.08 REMARK 500 LLP B 210 -108.91 -95.12 REMARK 500 THR B 354 122.28 84.61 REMARK 500 ILE B 368 69.00 -65.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO3 B 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NNP RELATED DB: PDB REMARK 900 SUPERCEDE THE OLD ENTRY 3NNP REMARK 900 RELATED ID: 4IXZ RELATED DB: PDB REMARK 900 RELATED ID: 4IY7 RELATED DB: PDB REMARK 900 RELATED ID: 4IYO RELATED DB: PDB DBREF 4IXS A 1 397 UNP Q5H4T8 Q5H4T8_XANOR 1 397 DBREF 4IXS B 1 397 UNP Q5H4T8 Q5H4T8_XANOR 1 397 SEQRES 1 A 397 MET SER ASN ARG THR THR HIS SER HIS ASP GLY ASP ARG SEQRES 2 A 397 ALA LEU SER LEU ALA THR LEU ALA ILE HIS GLY GLY GLN SEQRES 3 A 397 SER PRO ASP PRO SER THR GLY ALA VAL MET PRO PRO ILE SEQRES 4 A 397 TYR ALA THR SER THR TYR ALA GLN SER SER PRO GLY GLU SEQRES 5 A 397 HIS GLN GLY PHE GLU TYR SER ARG THR HIS ASN PRO THR SEQRES 6 A 397 ARG PHE ALA TYR GLU ARG CYS VAL ALA ALA LEU GLU GLY SEQRES 7 A 397 GLY THR ARG ALA PHE ALA PHE ALA SER GLY MET ALA ALA SEQRES 8 A 397 THR SER THR VAL MET GLU LEU LEU ASP ALA GLY SER HIS SEQRES 9 A 397 VAL VAL ALA MET ASP ASP LEU TYR GLY GLY THR PHE ARG SEQRES 10 A 397 LEU PHE GLU ARG VAL ARG ARG ARG THR ALA GLY LEU ASP SEQRES 11 A 397 PHE SER PHE VAL ASP LEU THR ASP PRO ALA ALA PHE LYS SEQRES 12 A 397 ALA ALA ILE ARG ALA ASP THR LYS MET VAL TRP ILE GLU SEQRES 13 A 397 THR PRO THR ASN PRO MET LEU LYS LEU VAL ASP ILE ALA SEQRES 14 A 397 ALA ILE ALA VAL ILE ALA ARG LYS HIS GLY LEU LEU THR SEQRES 15 A 397 VAL VAL ASP ASN THR PHE ALA SER PRO MET LEU GLN ARG SEQRES 16 A 397 PRO LEU SER LEU GLY ALA ASP LEU VAL VAL HIS SER ALA SEQRES 17 A 397 THR LLP TYR LEU ASN GLY HIS SER ASP MET VAL GLY GLY SEQRES 18 A 397 ILE ALA VAL VAL GLY ASP ASN ALA GLU LEU ALA GLU GLN SEQRES 19 A 397 MET ALA PHE LEU GLN ASN SER ILE GLY GLY VAL GLN GLY SEQRES 20 A 397 PRO PHE ASP SER PHE LEU ALA LEU ARG GLY LEU LYS THR SEQRES 21 A 397 LEU PRO LEU ARG MET ARG ALA HIS CYS GLU ASN ALA LEU SEQRES 22 A 397 ALA LEU ALA GLN TRP LEU GLU THR HIS PRO ALA ILE GLU SEQRES 23 A 397 LYS VAL ILE TYR PRO GLY LEU ALA SER HIS PRO GLN HIS SEQRES 24 A 397 VAL LEU ALA LYS ARG GLN MET SER GLY PHE GLY GLY ILE SEQRES 25 A 397 VAL SER ILE VAL LEU LYS GLY GLY PHE ASP ALA ALA LYS SEQRES 26 A 397 ARG PHE CYS GLU LYS THR GLU LEU PHE THR LEU ALA GLU SEQRES 27 A 397 SER LEU GLY GLY VAL GLU SER LEU VAL ASN HIS PRO ALA SEQRES 28 A 397 VAL MET THR HIS ALA SER ILE PRO VAL ALA ARG ARG GLU SEQRES 29 A 397 GLN LEU GLY ILE SER ASP ALA LEU VAL ARG LEU SER VAL SEQRES 30 A 397 GLY ILE GLU ASP LEU GLY ASP LEU ARG GLY ASP LEU GLU SEQRES 31 A 397 ARG ALA LEU VAL ASN GLN ASN SEQRES 1 B 397 MET SER ASN ARG THR THR HIS SER HIS ASP GLY ASP ARG SEQRES 2 B 397 ALA LEU SER LEU ALA THR LEU ALA ILE HIS GLY GLY GLN SEQRES 3 B 397 SER PRO ASP PRO SER THR GLY ALA VAL MET PRO PRO ILE SEQRES 4 B 397 TYR ALA THR SER THR TYR ALA GLN SER SER PRO GLY GLU SEQRES 5 B 397 HIS GLN GLY PHE GLU TYR SER ARG THR HIS ASN PRO THR SEQRES 6 B 397 ARG PHE ALA TYR GLU ARG CYS VAL ALA ALA LEU GLU GLY SEQRES 7 B 397 GLY THR ARG ALA PHE ALA PHE ALA SER GLY MET ALA ALA SEQRES 8 B 397 THR SER THR VAL MET GLU LEU LEU ASP ALA GLY SER HIS SEQRES 9 B 397 VAL VAL ALA MET ASP ASP LEU TYR GLY GLY THR PHE ARG SEQRES 10 B 397 LEU PHE GLU ARG VAL ARG ARG ARG THR ALA GLY LEU ASP SEQRES 11 B 397 PHE SER PHE VAL ASP LEU THR ASP PRO ALA ALA PHE LYS SEQRES 12 B 397 ALA ALA ILE ARG ALA ASP THR LYS MET VAL TRP ILE GLU SEQRES 13 B 397 THR PRO THR ASN PRO MET LEU LYS LEU VAL ASP ILE ALA SEQRES 14 B 397 ALA ILE ALA VAL ILE ALA ARG LYS HIS GLY LEU LEU THR SEQRES 15 B 397 VAL VAL ASP ASN THR PHE ALA SER PRO MET LEU GLN ARG SEQRES 16 B 397 PRO LEU SER LEU GLY ALA ASP LEU VAL VAL HIS SER ALA SEQRES 17 B 397 THR LLP TYR LEU ASN GLY HIS SER ASP MET VAL GLY GLY SEQRES 18 B 397 ILE ALA VAL VAL GLY ASP ASN ALA GLU LEU ALA GLU GLN SEQRES 19 B 397 MET ALA PHE LEU GLN ASN SER ILE GLY GLY VAL GLN GLY SEQRES 20 B 397 PRO PHE ASP SER PHE LEU ALA LEU ARG GLY LEU LYS THR SEQRES 21 B 397 LEU PRO LEU ARG MET ARG ALA HIS CYS GLU ASN ALA LEU SEQRES 22 B 397 ALA LEU ALA GLN TRP LEU GLU THR HIS PRO ALA ILE GLU SEQRES 23 B 397 LYS VAL ILE TYR PRO GLY LEU ALA SER HIS PRO GLN HIS SEQRES 24 B 397 VAL LEU ALA LYS ARG GLN MET SER GLY PHE GLY GLY ILE SEQRES 25 B 397 VAL SER ILE VAL LEU LYS GLY GLY PHE ASP ALA ALA LYS SEQRES 26 B 397 ARG PHE CYS GLU LYS THR GLU LEU PHE THR LEU ALA GLU SEQRES 27 B 397 SER LEU GLY GLY VAL GLU SER LEU VAL ASN HIS PRO ALA SEQRES 28 B 397 VAL MET THR HIS ALA SER ILE PRO VAL ALA ARG ARG GLU SEQRES 29 B 397 GLN LEU GLY ILE SER ASP ALA LEU VAL ARG LEU SER VAL SEQRES 30 B 397 GLY ILE GLU ASP LEU GLY ASP LEU ARG GLY ASP LEU GLU SEQRES 31 B 397 ARG ALA LEU VAL ASN GLN ASN MODRES 4IXS LLP A 210 LYS MODRES 4IXS LLP B 210 LYS HET LLP A 210 24 HET LLP B 210 24 HET GOL A 401 6 HET CO3 B 401 4 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM GOL GLYCEROL HETNAM CO3 CARBONATE ION HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 LLP 2(C14 H22 N3 O7 P) FORMUL 3 GOL C3 H8 O3 FORMUL 4 CO3 C O3 2- FORMUL 5 HOH *273(H2 O) HELIX 1 1 SER A 16 GLY A 24 1 9 HELIX 2 2 ASN A 63 GLY A 78 1 16 HELIX 3 3 SER A 87 GLU A 97 1 11 HELIX 4 4 TYR A 112 VAL A 122 1 11 HELIX 5 5 VAL A 122 GLY A 128 1 7 HELIX 6 6 ASP A 138 ALA A 144 1 7 HELIX 7 7 ASP A 167 HIS A 178 1 12 HELIX 8 8 ARG A 195 GLY A 200 5 6 HELIX 9 9 ASN A 228 GLY A 243 1 16 HELIX 10 10 GLY A 247 THR A 260 1 14 HELIX 11 11 THR A 260 THR A 281 1 22 HELIX 12 12 GLN A 298 MET A 306 1 9 HELIX 13 13 GLY A 319 THR A 331 1 13 HELIX 14 14 ASP A 381 VAL A 394 1 14 HELIX 15 15 SER B 16 GLY B 24 1 9 HELIX 16 16 ASN B 63 GLY B 78 1 16 HELIX 17 17 SER B 87 GLU B 97 1 11 HELIX 18 18 TYR B 112 VAL B 122 1 11 HELIX 19 19 VAL B 122 GLY B 128 1 7 HELIX 20 20 ASP B 138 ILE B 146 1 9 HELIX 21 21 ASP B 167 HIS B 178 1 12 HELIX 22 22 ALA B 189 GLN B 194 1 6 HELIX 23 23 ARG B 195 GLY B 200 5 6 HELIX 24 24 ASN B 228 GLY B 243 1 16 HELIX 25 25 GLY B 247 LYS B 259 1 13 HELIX 26 26 THR B 260 GLU B 280 1 21 HELIX 27 27 GLN B 298 MET B 306 1 9 HELIX 28 28 GLY B 319 THR B 331 1 13 HELIX 29 29 PRO B 359 GLY B 367 1 9 HELIX 30 30 ASP B 381 VAL B 394 1 14 SHEET 1 A 7 ARG A 81 PHE A 85 0 SHEET 2 A 7 GLY A 221 VAL A 225 -1 O VAL A 225 N ARG A 81 SHEET 3 A 7 LEU A 203 SER A 207 -1 N HIS A 206 O ILE A 222 SHEET 4 A 7 LEU A 181 ASP A 185 1 N VAL A 184 O VAL A 205 SHEET 5 A 7 THR A 150 GLU A 156 1 N ILE A 155 O ASP A 185 SHEET 6 A 7 HIS A 104 MET A 108 1 N HIS A 104 O LYS A 151 SHEET 7 A 7 ASP A 130 VAL A 134 1 O ASP A 130 N VAL A 105 SHEET 1 B 5 ILE A 285 ILE A 289 0 SHEET 2 B 5 ILE A 312 LEU A 317 -1 O SER A 314 N ILE A 289 SHEET 3 B 5 LEU A 372 SER A 376 -1 O LEU A 375 N VAL A 313 SHEET 4 B 5 LEU A 346 ASN A 348 -1 N LEU A 346 O SER A 376 SHEET 5 B 5 THR A 335 LEU A 336 1 N THR A 335 O VAL A 347 SHEET 1 C 7 ARG B 81 PHE B 85 0 SHEET 2 C 7 GLY B 221 VAL B 225 -1 O GLY B 221 N PHE B 85 SHEET 3 C 7 LEU B 203 SER B 207 -1 N VAL B 204 O VAL B 224 SHEET 4 C 7 LEU B 181 ASP B 185 1 N VAL B 184 O VAL B 205 SHEET 5 C 7 THR B 150 GLU B 156 1 N ILE B 155 O VAL B 183 SHEET 6 C 7 HIS B 104 MET B 108 1 N HIS B 104 O LYS B 151 SHEET 7 C 7 ASP B 130 VAL B 134 1 O ASP B 130 N VAL B 105 SHEET 1 D 5 ILE B 285 ILE B 289 0 SHEET 2 D 5 ILE B 312 LEU B 317 -1 O SER B 314 N ILE B 289 SHEET 3 D 5 LEU B 372 SER B 376 -1 O LEU B 375 N VAL B 313 SHEET 4 D 5 LEU B 346 ASN B 348 -1 N LEU B 346 O SER B 376 SHEET 5 D 5 THR B 335 LEU B 336 1 N THR B 335 O VAL B 347 LINK C THR A 209 N LLP A 210 1555 1555 1.31 LINK C LLP A 210 N TYR A 211 1555 1555 1.31 LINK C THR B 209 N LLP B 210 1555 1555 1.31 LINK C LLP B 210 N TYR B 211 1555 1555 1.31 CISPEP 1 THR A 157 PRO A 158 0 -2.31 CISPEP 2 ASN A 160 PRO A 161 0 -2.55 CISPEP 3 THR B 157 PRO B 158 0 -6.81 CISPEP 4 ASN B 160 PRO B 161 0 10.79 SITE 1 AC1 7 ALA A 267 ASN A 271 ILE A 379 GLU A 380 SITE 2 AC1 7 ASP A 381 LEU A 382 ARG B 266 SITE 1 AC2 7 TYR B 112 ASN B 160 LLP B 210 GLU B 338 SITE 2 AC2 7 SER B 339 THR B 354 ARG B 374 CRYST1 85.722 124.357 146.164 90.00 90.00 90.00 C 2 2 21 16 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 0.011666 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008041 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006842 0.00000