HEADER LYASE 24-JUN-10 3NNP OBSLTE 29-JAN-14 3NNP 4IXS TITLE NATIVE STRUCTURE OF XOMETC, A CYSTATHIONINE C-LYASE PROTEIN FROM TITLE 2 XANTHOMONAS ORYZAE PV.ORYZAE, AT PH 5.2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTATHIONINE GAMMA-LYASE-LIKE PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: XOMETC; COMPND 5 EC: 4.4.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS ORYZAE PV. ORYZAE; SOURCE 3 ORGANISM_TAXID: 291331; SOURCE 4 STRAIN: KACC10331; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS XOMETC, LYASE, NATIVE, CYS-MET METABOLISM PLP-DEPENDENT ENZYME KEYWDS 2 FAMILY, CYSTATHIONINE GAMMA LYASE, PYRIDOXAL-PHOSPHATE (PLP) EXPDTA X-RAY DIFFRACTION AUTHOR H.P.T.NGO,J.K.KIM,L.W.KANG REVDAT 2 29-JAN-14 3NNP 1 OBSLTE VERSN REVDAT 1 07-JUL-10 3NNP 0 JRNL AUTH H.P.T.NGO,J.K.KIM,L.W.KANG JRNL TITL CRYSTAL STRUCTURE OF XOMETC, A CYSTATHIONINE C-LYASE PROTEIN JRNL TITL 2 FROM XANTHOMONAS ORYZAE PV.ORYZAE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.29 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 116 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL 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) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1750 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5496 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 285 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5671 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7701 ; 1.945 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 738 ; 7.181 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 224 ;36.931 ;22.946 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 916 ;19.561 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 43 ;22.368 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 894 ; 0.148 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4245 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2662 ; 0.224 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3826 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 343 ; 0.150 ; 0.200 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): 144 ; 0.215 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.217 ; 0.200 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): 3750 ; 1.070 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5830 ; 1.765 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2128 ; 3.017 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1866 ; 4.530 ; 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 : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3NNP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JUN-10. REMARK 100 THE RCSB ID CODE IS RCSB060055. 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) : 100.0 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) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.4000 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) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.990 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 (%): 45.79 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 PH 5.2, 0.2M SODIUM THIOCYANATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.0K 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: 20720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42310 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 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 531 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 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 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 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 1.91 REMARK 500 NH1 ARG B 363 O HOH B 448 2.19 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 O HOH B 552 O HOH B 552 3655 2.19 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 B 66 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 66 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 71 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 123 CG - CD - NE ANGL. DEV. = -12.7 DEGREES REMARK 500 ARG B 123 NE - CZ - NH1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG B 123 NE - CZ - NH2 ANGL. DEV. = -7.3 DEGREES REMARK 500 VAL B 153 CB - CA - C ANGL. DEV. = -13.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 60 -43.71 73.16 REMARK 500 ASP A 110 45.62 -83.29 REMARK 500 VAL A 122 -59.17 -125.70 REMARK 500 ASP A 135 87.22 -65.78 REMARK 500 SER A 190 163.19 71.32 REMARK 500 LYS A 210 -113.24 -92.89 REMARK 500 ASN A 228 88.79 -151.94 REMARK 500 MET A 353 -115.90 -83.64 REMARK 500 ASP B 135 88.33 -67.92 REMARK 500 SER B 190 162.30 79.14 REMARK 500 LYS B 210 -110.67 -90.96 REMARK 500 MET B 353 -102.76 -106.90 REMARK 500 ILE B 368 67.22 -66.84 REMARK 500 SER B 369 154.45 -47.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 HIS B 206 SER B 207 149.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 VAL B 95 23.3 L L OUTSIDE RANGE REMARK 500 ARG B 125 16.6 L L OUTSIDE RANGE REMARK 500 VAL B 316 23.9 L L OUTSIDE RANGE 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 527 DISTANCE = 5.18 ANGSTROMS REMARK 525 HOH B 542 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 398 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 399 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLP B 398 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BCT B 399 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3E6G RELATED DB: PDB REMARK 900 LOW RESOLUTION OF NATIVE STRUCTURE AT PH 5.2 REMARK 900 RELATED ID: 3NMY RELATED DB: PDB REMARK 900 NATIVE STRUCTURE AT PH 9.0 DBREF 3NNP A 1 397 UNP Q5H4T8 Q5H4T8_XANOR 1 397 DBREF 3NNP B 1 397 UNP Q5H4T8 Q5H4T8_XANOR 1 397 SEQADV 3NNP GLY A -2 UNP Q5H4T8 EXPRESSION TAG SEQADV 3NNP SER A -1 UNP Q5H4T8 EXPRESSION TAG SEQADV 3NNP HIS A 0 UNP Q5H4T8 EXPRESSION TAG SEQADV 3NNP GLY B -2 UNP Q5H4T8 EXPRESSION TAG SEQADV 3NNP SER B -1 UNP Q5H4T8 EXPRESSION TAG SEQADV 3NNP HIS B 0 UNP Q5H4T8 EXPRESSION TAG SEQRES 1 A 400 GLY SER HIS MET SER ASN ARG THR THR HIS SER HIS ASP SEQRES 2 A 400 GLY ASP ARG ALA LEU SER LEU ALA THR LEU ALA ILE HIS SEQRES 3 A 400 GLY GLY GLN SER PRO ASP PRO SER THR GLY ALA VAL MET SEQRES 4 A 400 PRO PRO ILE TYR ALA THR SER THR TYR ALA GLN SER SER SEQRES 5 A 400 PRO GLY GLU HIS GLN GLY PHE GLU TYR SER ARG THR HIS SEQRES 6 A 400 ASN PRO THR ARG PHE ALA TYR GLU ARG CYS VAL ALA ALA SEQRES 7 A 400 LEU GLU GLY GLY THR ARG ALA PHE ALA PHE ALA SER GLY SEQRES 8 A 400 MET ALA ALA THR SER THR VAL MET GLU LEU LEU ASP ALA SEQRES 9 A 400 GLY SER HIS VAL VAL ALA MET ASP ASP LEU TYR GLY GLY SEQRES 10 A 400 THR PHE ARG LEU PHE GLU ARG VAL ARG ARG ARG THR ALA SEQRES 11 A 400 GLY LEU ASP PHE SER PHE VAL ASP LEU THR ASP PRO ALA SEQRES 12 A 400 ALA PHE LYS ALA ALA ILE ARG ALA ASP THR LYS MET VAL SEQRES 13 A 400 TRP ILE GLU THR PRO THR ASN PRO MET LEU LYS LEU VAL SEQRES 14 A 400 ASP ILE ALA ALA ILE ALA VAL ILE ALA ARG LYS HIS GLY SEQRES 15 A 400 LEU LEU THR VAL VAL ASP ASN THR PHE ALA SER PRO MET SEQRES 16 A 400 LEU GLN ARG PRO LEU SER LEU GLY ALA ASP LEU VAL VAL SEQRES 17 A 400 HIS SER ALA THR LYS TYR LEU ASN GLY HIS SER ASP MET SEQRES 18 A 400 VAL GLY GLY ILE ALA VAL VAL GLY ASP ASN ALA GLU LEU SEQRES 19 A 400 ALA GLU GLN MET ALA PHE LEU GLN ASN SER ILE GLY GLY SEQRES 20 A 400 VAL GLN GLY PRO PHE ASP SER PHE LEU ALA LEU ARG GLY SEQRES 21 A 400 LEU LYS THR LEU PRO LEU ARG MET ARG ALA HIS CYS GLU SEQRES 22 A 400 ASN ALA LEU ALA LEU ALA GLN TRP LEU GLU THR HIS PRO SEQRES 23 A 400 ALA ILE GLU LYS VAL ILE TYR PRO GLY LEU ALA SER HIS SEQRES 24 A 400 PRO GLN HIS VAL LEU ALA LYS ARG GLN MET SER GLY PHE SEQRES 25 A 400 GLY GLY ILE VAL SER ILE VAL LEU LYS GLY GLY PHE ASP SEQRES 26 A 400 ALA ALA LYS ARG PHE CYS GLU LYS THR GLU LEU PHE THR SEQRES 27 A 400 LEU ALA GLU SER LEU GLY GLY VAL GLU SER LEU VAL ASN SEQRES 28 A 400 HIS PRO ALA VAL MET THR HIS ALA SER ILE PRO VAL ALA SEQRES 29 A 400 ARG ARG GLU GLN LEU GLY ILE SER ASP ALA LEU VAL ARG SEQRES 30 A 400 LEU SER VAL GLY ILE GLU ASP LEU GLY ASP LEU ARG GLY SEQRES 31 A 400 ASP LEU GLU ARG ALA LEU VAL ASN GLN ASN SEQRES 1 B 400 GLY SER HIS MET SER ASN ARG THR THR HIS SER HIS ASP SEQRES 2 B 400 GLY ASP ARG ALA LEU SER LEU ALA THR LEU ALA ILE HIS SEQRES 3 B 400 GLY GLY GLN SER PRO ASP PRO SER THR GLY ALA VAL MET SEQRES 4 B 400 PRO PRO ILE TYR ALA THR SER THR TYR ALA GLN SER SER SEQRES 5 B 400 PRO GLY GLU HIS GLN GLY PHE GLU TYR SER ARG THR HIS SEQRES 6 B 400 ASN PRO THR ARG PHE ALA TYR GLU ARG CYS VAL ALA ALA SEQRES 7 B 400 LEU GLU GLY GLY THR ARG ALA PHE ALA PHE ALA SER GLY SEQRES 8 B 400 MET ALA ALA THR SER THR VAL MET GLU LEU LEU ASP ALA SEQRES 9 B 400 GLY SER HIS VAL VAL ALA MET ASP ASP LEU TYR GLY GLY SEQRES 10 B 400 THR PHE ARG LEU PHE GLU ARG VAL ARG ARG ARG THR ALA SEQRES 11 B 400 GLY LEU ASP PHE SER PHE VAL ASP LEU THR ASP PRO ALA SEQRES 12 B 400 ALA PHE LYS ALA ALA ILE ARG ALA ASP THR LYS MET VAL SEQRES 13 B 400 TRP ILE GLU THR PRO THR ASN PRO MET LEU LYS LEU VAL SEQRES 14 B 400 ASP ILE ALA ALA ILE ALA VAL ILE ALA ARG LYS HIS GLY SEQRES 15 B 400 LEU LEU THR VAL VAL ASP ASN THR PHE ALA SER PRO MET SEQRES 16 B 400 LEU GLN ARG PRO LEU SER LEU GLY ALA ASP LEU VAL VAL SEQRES 17 B 400 HIS SER ALA THR LYS TYR LEU ASN GLY HIS SER ASP MET SEQRES 18 B 400 VAL GLY GLY ILE ALA VAL VAL GLY ASP ASN ALA GLU LEU SEQRES 19 B 400 ALA GLU GLN MET ALA PHE LEU GLN ASN SER ILE GLY GLY SEQRES 20 B 400 VAL GLN GLY PRO PHE ASP SER PHE LEU ALA LEU ARG GLY SEQRES 21 B 400 LEU LYS THR LEU PRO LEU ARG MET ARG ALA HIS CYS GLU SEQRES 22 B 400 ASN ALA LEU ALA LEU ALA GLN TRP LEU GLU THR HIS PRO SEQRES 23 B 400 ALA ILE GLU LYS VAL ILE TYR PRO GLY LEU ALA SER HIS SEQRES 24 B 400 PRO GLN HIS VAL LEU ALA LYS ARG GLN MET SER GLY PHE SEQRES 25 B 400 GLY GLY ILE VAL SER ILE VAL LEU LYS GLY GLY PHE ASP SEQRES 26 B 400 ALA ALA LYS ARG PHE CYS GLU LYS THR GLU LEU PHE THR SEQRES 27 B 400 LEU ALA GLU SER LEU GLY GLY VAL GLU SER LEU VAL ASN SEQRES 28 B 400 HIS PRO ALA VAL MET THR HIS ALA SER ILE PRO VAL ALA SEQRES 29 B 400 ARG ARG GLU GLN LEU GLY ILE SER ASP ALA LEU VAL ARG SEQRES 30 B 400 LEU SER VAL GLY ILE GLU ASP LEU GLY ASP LEU ARG GLY SEQRES 31 B 400 ASP LEU GLU ARG ALA LEU VAL ASN GLN ASN HET PLP A 398 15 HET GOL A 399 6 HET PLP B 398 15 HET BCT B 399 4 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM GOL GLYCEROL HETNAM BCT BICARBONATE ION HETSYN PLP VITAMIN B6 PHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 4 GOL C3 H8 O3 FORMUL 6 BCT C H O3 1- FORMUL 7 HOH *285(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 LYS A 259 1 13 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 ARG B 195 GLY B 200 5 6 HELIX 23 23 ASN B 228 GLY B 243 1 16 HELIX 24 24 GLY B 247 GLU B 280 1 34 HELIX 25 25 GLN B 298 MET B 306 1 9 HELIX 26 26 GLY B 319 THR B 331 1 13 HELIX 27 27 PRO B 359 GLY B 367 1 9 HELIX 28 28 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 VAL A 106 O TRP A 154 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 VAL B 316 N GLU B 286 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 NZ LYS A 210 C4A PLP A 398 1555 1555 1.87 LINK NZ LYS B 210 C4A PLP B 398 1555 1555 1.65 CISPEP 1 THR A 157 PRO A 158 0 -3.54 CISPEP 2 ASN A 160 PRO A 161 0 -4.14 CISPEP 3 THR B 157 PRO B 158 0 -7.68 CISPEP 4 ASN B 160 PRO B 161 0 9.95 SITE 1 AC1 10 ARG A 60 SER A 87 GLY A 88 MET A 89 SITE 2 AC1 10 TYR A 112 ASP A 185 THR A 187 SER A 207 SITE 3 AC1 10 THR A 209 LYS A 210 SITE 1 AC2 8 ALA A 267 ASN A 271 ILE A 379 GLU A 380 SITE 2 AC2 8 ASP A 381 LEU A 382 HOH A 515 ARG B 266 SITE 1 AC3 13 ARG B 60 SER B 87 GLY B 88 MET B 89 SITE 2 AC3 13 TYR B 112 ASN B 160 ASP B 185 THR B 187 SITE 3 AC3 13 SER B 207 THR B 209 LYS B 210 GLY B 220 SITE 4 AC3 13 HOH B 436 SITE 1 AC4 6 ASN B 160 LYS B 210 GLU B 338 SER B 339 SITE 2 AC4 6 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