HEADER LYASE 13-JAN-10 3LDV TITLE 1.77 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE TITLE 2 DECARBOXYLASE FROM VIBRIO CHOLERAE O1 BIOVAR ELTOR STR. N16961 COMPND MOL_ID: 1; COMPND 2 MOLECULE: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: OROTIDINE 5'-PHOSPHATE DECARBOXYLASE; COMPND 5 SYNONYM: OMP DECARBOXYLASE, OMPDCASE, OMPDECASE; COMPND 6 EC: 4.1.1.23; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE O1 BIOVAR EL TOR; SOURCE 3 ORGANISM_TAXID: 243277; SOURCE 4 STRAIN: N16961; SOURCE 5 GENE: PYRF, VC_1911; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)CODONPLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS OROTIDINE 5'-PHOSPHATE DECARBOXYLASE, STRUCTURAL GENOMICS, INFECTIOUS KEYWDS 2 DISEASES, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES, KEYWDS 3 DECARBOXYLASE, LYASE, PYRIMIDINE BIOSYNTHESIS, CSGID EXPDTA X-RAY DIFFRACTION AUTHOR A.S.HALAVATY,L.SHUVALOVA,G.MINASOV,I.DUBROVSKA,J.WINSOR,E.M.GLASS, AUTHOR 2 S.N.PETERSON,W.F.ANDERSON,CENTER FOR STRUCTURAL GENOMICS OF AUTHOR 3 INFECTIOUS DISEASES (CSGID) REVDAT 3 06-SEP-23 3LDV 1 REMARK SEQADV LINK REVDAT 2 01-NOV-17 3LDV 1 REMARK REVDAT 1 26-JAN-10 3LDV 0 JRNL AUTH A.S.HALAVATY,L.SHUVALOVA,G.MINASOV,I.DUBROVSKA,J.WINSOR, JRNL AUTH 2 E.M.GLASS,S.N.PETERSON,W.F.ANDERSON, JRNL AUTH 3 CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES JRNL AUTH 4 (CSGID) JRNL TITL 1.77 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF OROTIDINE JRNL TITL 2 5'-PHOSPHATE DECARBOXYLASE FROM VIBRIO CHOLERAE O1 BIOVAR JRNL TITL 3 ELTOR STR. N16961 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 41524 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) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2205 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2912 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 164 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3457 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 593 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.82000 REMARK 3 B22 (A**2) : -0.43000 REMARK 3 B33 (A**2) : -2.38000 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): 0.115 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.901 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3718 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2534 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5065 ; 1.383 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6232 ; 0.858 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 496 ; 3.529 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 152 ;31.780 ;24.211 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 661 ;10.316 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;10.690 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 581 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4244 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 712 ; 0.001 ; 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): 2395 ; 0.719 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 962 ; 0.223 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3886 ; 1.273 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1323 ; 2.120 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1179 ; 3.612 ; 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 : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 50 REMARK 3 ORIGIN FOR THE GROUP (A): 27.9230 67.5135 16.2993 REMARK 3 T TENSOR REMARK 3 T11: 0.0336 T22: 0.0623 REMARK 3 T33: 0.1027 T12: -0.0035 REMARK 3 T13: 0.0225 T23: 0.0084 REMARK 3 L TENSOR REMARK 3 L11: 1.4040 L22: 2.4001 REMARK 3 L33: 2.8106 L12: 0.0491 REMARK 3 L13: 0.5987 L23: -1.3708 REMARK 3 S TENSOR REMARK 3 S11: -0.0096 S12: 0.0981 S13: 0.1385 REMARK 3 S21: -0.0958 S22: -0.1108 S23: -0.1445 REMARK 3 S31: -0.0593 S32: 0.2017 S33: 0.1204 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 51 A 134 REMARK 3 ORIGIN FOR THE GROUP (A): 14.7595 61.9597 26.8240 REMARK 3 T TENSOR REMARK 3 T11: 0.0007 T22: 0.0582 REMARK 3 T33: 0.0555 T12: 0.0001 REMARK 3 T13: 0.0029 T23: -0.0171 REMARK 3 L TENSOR REMARK 3 L11: 0.8915 L22: 1.4618 REMARK 3 L33: 2.1328 L12: 0.0479 REMARK 3 L13: 0.1141 L23: -0.8470 REMARK 3 S TENSOR REMARK 3 S11: 0.0099 S12: -0.0770 S13: 0.0411 REMARK 3 S21: -0.0189 S22: 0.0268 S23: 0.0559 REMARK 3 S31: 0.0062 S32: -0.1850 S33: -0.0367 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 135 A 207 REMARK 3 ORIGIN FOR THE GROUP (A): 9.2963 56.0704 11.1740 REMARK 3 T TENSOR REMARK 3 T11: 0.0590 T22: 0.0655 REMARK 3 T33: 0.1033 T12: -0.0044 REMARK 3 T13: -0.0141 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 1.2759 L22: 0.5976 REMARK 3 L33: 4.0491 L12: 0.4850 REMARK 3 L13: 0.7200 L23: 0.4239 REMARK 3 S TENSOR REMARK 3 S11: -0.0111 S12: 0.0199 S13: -0.0454 REMARK 3 S21: -0.1358 S22: 0.0525 S23: 0.0107 REMARK 3 S31: 0.1675 S32: -0.0353 S33: -0.0414 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 208 A 230 REMARK 3 ORIGIN FOR THE GROUP (A): 25.3478 63.9318 2.6745 REMARK 3 T TENSOR REMARK 3 T11: 0.1856 T22: 0.2230 REMARK 3 T33: 0.0864 T12: -0.0467 REMARK 3 T13: 0.0313 T23: -0.0323 REMARK 3 L TENSOR REMARK 3 L11: 7.5751 L22: 2.7906 REMARK 3 L33: 5.3653 L12: -0.8469 REMARK 3 L13: 0.4096 L23: -2.0490 REMARK 3 S TENSOR REMARK 3 S11: -0.0888 S12: 0.9398 S13: 0.1362 REMARK 3 S21: -0.6097 S22: 0.0421 S23: -0.3150 REMARK 3 S31: 0.5059 S32: 0.4631 S33: 0.0467 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 43 REMARK 3 ORIGIN FOR THE GROUP (A): 30.8908 62.8899 45.0979 REMARK 3 T TENSOR REMARK 3 T11: 0.0490 T22: 0.0965 REMARK 3 T33: 0.0941 T12: -0.0369 REMARK 3 T13: -0.0268 T23: -0.0241 REMARK 3 L TENSOR REMARK 3 L11: 1.7929 L22: 2.0705 REMARK 3 L33: 3.8159 L12: -0.1858 REMARK 3 L13: 1.3802 L23: -1.1479 REMARK 3 S TENSOR REMARK 3 S11: -0.0423 S12: -0.1333 S13: 0.0918 REMARK 3 S21: 0.2000 S22: -0.0889 S23: -0.1787 REMARK 3 S31: -0.2458 S32: 0.1472 S33: 0.1312 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 44 B 140 REMARK 3 ORIGIN FOR THE GROUP (A): 27.1751 50.6659 33.1525 REMARK 3 T TENSOR REMARK 3 T11: 0.0161 T22: 0.0490 REMARK 3 T33: 0.0729 T12: 0.0020 REMARK 3 T13: 0.0171 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.8691 L22: 1.3648 REMARK 3 L33: 1.6634 L12: 0.1491 REMARK 3 L13: 0.1216 L23: -0.5431 REMARK 3 S TENSOR REMARK 3 S11: -0.0005 S12: -0.0386 S13: -0.0359 REMARK 3 S21: -0.0976 S22: -0.0326 S23: -0.1285 REMARK 3 S31: 0.1409 S32: 0.0809 S33: 0.0331 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 141 B 194 REMARK 3 ORIGIN FOR THE GROUP (A): 21.2766 42.5421 45.7130 REMARK 3 T TENSOR REMARK 3 T11: 0.0536 T22: 0.0588 REMARK 3 T33: 0.0769 T12: -0.0013 REMARK 3 T13: -0.0033 T23: 0.0039 REMARK 3 L TENSOR REMARK 3 L11: 1.1673 L22: 2.7706 REMARK 3 L33: 2.9720 L12: 0.3080 REMARK 3 L13: -0.3458 L23: 0.0149 REMARK 3 S TENSOR REMARK 3 S11: -0.0176 S12: -0.1720 S13: 0.0008 REMARK 3 S21: 0.2095 S22: -0.0289 S23: 0.0036 REMARK 3 S31: 0.1565 S32: -0.0138 S33: 0.0464 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 195 B 231 REMARK 3 ORIGIN FOR THE GROUP (A): 27.5257 54.8407 56.0221 REMARK 3 T TENSOR REMARK 3 T11: 0.1075 T22: 0.1307 REMARK 3 T33: 0.0744 T12: -0.0515 REMARK 3 T13: -0.0124 T23: -0.0210 REMARK 3 L TENSOR REMARK 3 L11: 1.0668 L22: 3.7076 REMARK 3 L33: 1.2850 L12: 0.5914 REMARK 3 L13: 0.4946 L23: 0.2474 REMARK 3 S TENSOR REMARK 3 S11: 0.0762 S12: -0.2337 S13: 0.0656 REMARK 3 S21: 0.4487 S22: -0.1231 S23: -0.0428 REMARK 3 S31: -0.0200 S32: -0.0518 S33: 0.0469 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B REMARK 3 FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U REMARK 3 FACTORS. REMARK 4 REMARK 4 3LDV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000057155. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : DIAMOND[111] REMARK 200 OPTICS : BE LENSES/DIAMOND LAUE MONO REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43787 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.1500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.56500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.770 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: 1L2U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 7MG/ML PROTEIN, THE PACT SUITE REMARK 280 CONDITION #34 (C10), 1:1 V/V RATIO, PH 7.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 23.65000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.59150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.33750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.59150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.65000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.33750 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: 4010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -61.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -23 REMARK 465 HIS A -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 SER A -16 REMARK 465 SER A -15 REMARK 465 GLY A -14 REMARK 465 VAL A -13 REMARK 465 ASP A -12 REMARK 465 LEU A -11 REMARK 465 GLY A -10 REMARK 465 THR A -9 REMARK 465 GLU A -8 REMARK 465 ASN A -7 REMARK 465 LEU A -6 REMARK 465 TYR A -5 REMARK 465 PHE A -4 REMARK 465 GLN A -3 REMARK 465 SER A -2 REMARK 465 ASN A -1 REMARK 465 VAL A 231 REMARK 465 MET B -23 REMARK 465 HIS B -22 REMARK 465 HIS B -21 REMARK 465 HIS B -20 REMARK 465 HIS B -19 REMARK 465 HIS B -18 REMARK 465 HIS B -17 REMARK 465 SER B -16 REMARK 465 SER B -15 REMARK 465 GLY B -14 REMARK 465 VAL B -13 REMARK 465 ASP B -12 REMARK 465 LEU B -11 REMARK 465 GLY B -10 REMARK 465 THR B -9 REMARK 465 GLU B -8 REMARK 465 ASN B -7 REMARK 465 LEU B -6 REMARK 465 TYR B -5 REMARK 465 PHE B -4 REMARK 465 GLN B -3 REMARK 465 SER B -2 REMARK 465 ASN B -1 REMARK 465 ALA B 0 REMARK 465 MET B 1 REMARK 465 GLY B 184 REMARK 465 SER B 185 REMARK 465 GLU B 186 REMARK 465 GLN B 187 REMARK 465 GLY B 188 REMARK 465 ASP B 189 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 THR A 117 -91.76 -95.76 REMARK 500 ASP B 60 72.49 -102.22 REMARK 500 THR B 117 -95.70 -96.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 232 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 26 OD1 REMARK 620 2 HOH A 330 O 84.2 REMARK 620 3 HOH A 487 O 95.1 168.3 REMARK 620 4 HOH A 516 O 89.6 86.9 104.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 232 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 233 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 234 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 232 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 233 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: IDP90525 RELATED DB: TARGETDB DBREF 3LDV A 1 231 UNP Q9KQT7 PYRF_VIBCH 1 231 DBREF 3LDV B 1 231 UNP Q9KQT7 PYRF_VIBCH 1 231 SEQADV 3LDV MET A -23 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV HIS A -22 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV HIS A -21 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV HIS A -20 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV HIS A -19 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV HIS A -18 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV HIS A -17 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV SER A -16 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV SER A -15 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV GLY A -14 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV VAL A -13 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV ASP A -12 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV LEU A -11 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV GLY A -10 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV THR A -9 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV GLU A -8 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV ASN A -7 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV LEU A -6 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV TYR A -5 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV PHE A -4 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV GLN A -3 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV SER A -2 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV ASN A -1 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV ALA A 0 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV MET B -23 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV HIS B -22 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV HIS B -21 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV HIS B -20 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV HIS B -19 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV HIS B -18 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV HIS B -17 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV SER B -16 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV SER B -15 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV GLY B -14 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV VAL B -13 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV ASP B -12 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV LEU B -11 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV GLY B -10 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV THR B -9 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV GLU B -8 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV ASN B -7 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV LEU B -6 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV TYR B -5 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV PHE B -4 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV GLN B -3 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV SER B -2 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV ASN B -1 UNP Q9KQT7 EXPRESSION TAG SEQADV 3LDV ALA B 0 UNP Q9KQT7 EXPRESSION TAG SEQRES 1 A 255 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 255 GLY THR GLU ASN LEU TYR PHE GLN SER ASN ALA MET ASN SEQRES 3 A 255 ASP PRO LYS VAL ILE VAL ALA LEU ASP TYR ASP ASN LEU SEQRES 4 A 255 ALA ASP ALA LEU ALA PHE VAL ASP LYS ILE ASP PRO SER SEQRES 5 A 255 THR CYS ARG LEU LYS VAL GLY LYS GLU MET PHE THR LEU SEQRES 6 A 255 PHE GLY PRO ASP PHE VAL ARG GLU LEU HIS LYS ARG GLY SEQRES 7 A 255 PHE SER VAL PHE LEU ASP LEU LYS PHE HIS ASP ILE PRO SEQRES 8 A 255 ASN THR CYS SER LYS ALA VAL LYS ALA ALA ALA GLU LEU SEQRES 9 A 255 GLY VAL TRP MET VAL ASN VAL HIS ALA SER GLY GLY GLU SEQRES 10 A 255 ARG MET MET ALA ALA SER ARG GLU ILE LEU GLU PRO TYR SEQRES 11 A 255 GLY LYS GLU ARG PRO LEU LEU ILE GLY VAL THR VAL LEU SEQRES 12 A 255 THR SER MET GLU SER ALA ASP LEU GLN GLY ILE GLY ILE SEQRES 13 A 255 LEU SER ALA PRO GLN ASP HIS VAL LEU ARG LEU ALA THR SEQRES 14 A 255 LEU THR LYS ASN ALA GLY LEU ASP GLY VAL VAL CYS SER SEQRES 15 A 255 ALA GLN GLU ALA SER LEU LEU LYS GLN HIS LEU GLY ARG SEQRES 16 A 255 GLU PHE LYS LEU VAL THR PRO GLY ILE ARG PRO ALA GLY SEQRES 17 A 255 SER GLU GLN GLY ASP GLN ARG ARG ILE MET THR PRO ALA SEQRES 18 A 255 GLN ALA ILE ALA SER GLY SER ASP TYR LEU VAL ILE GLY SEQRES 19 A 255 ARG PRO ILE THR GLN ALA ALA HIS PRO GLU VAL VAL LEU SEQRES 20 A 255 GLU GLU ILE ASN SER SER LEU VAL SEQRES 1 B 255 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 B 255 GLY THR GLU ASN LEU TYR PHE GLN SER ASN ALA MET ASN SEQRES 3 B 255 ASP PRO LYS VAL ILE VAL ALA LEU ASP TYR ASP ASN LEU SEQRES 4 B 255 ALA ASP ALA LEU ALA PHE VAL ASP LYS ILE ASP PRO SER SEQRES 5 B 255 THR CYS ARG LEU LYS VAL GLY LYS GLU MET PHE THR LEU SEQRES 6 B 255 PHE GLY PRO ASP PHE VAL ARG GLU LEU HIS LYS ARG GLY SEQRES 7 B 255 PHE SER VAL PHE LEU ASP LEU LYS PHE HIS ASP ILE PRO SEQRES 8 B 255 ASN THR CYS SER LYS ALA VAL LYS ALA ALA ALA GLU LEU SEQRES 9 B 255 GLY VAL TRP MET VAL ASN VAL HIS ALA SER GLY GLY GLU SEQRES 10 B 255 ARG MET MET ALA ALA SER ARG GLU ILE LEU GLU PRO TYR SEQRES 11 B 255 GLY LYS GLU ARG PRO LEU LEU ILE GLY VAL THR VAL LEU SEQRES 12 B 255 THR SER MET GLU SER ALA ASP LEU GLN GLY ILE GLY ILE SEQRES 13 B 255 LEU SER ALA PRO GLN ASP HIS VAL LEU ARG LEU ALA THR SEQRES 14 B 255 LEU THR LYS ASN ALA GLY LEU ASP GLY VAL VAL CYS SER SEQRES 15 B 255 ALA GLN GLU ALA SER LEU LEU LYS GLN HIS LEU GLY ARG SEQRES 16 B 255 GLU PHE LYS LEU VAL THR PRO GLY ILE ARG PRO ALA GLY SEQRES 17 B 255 SER GLU GLN GLY ASP GLN ARG ARG ILE MET THR PRO ALA SEQRES 18 B 255 GLN ALA ILE ALA SER GLY SER ASP TYR LEU VAL ILE GLY SEQRES 19 B 255 ARG PRO ILE THR GLN ALA ALA HIS PRO GLU VAL VAL LEU SEQRES 20 B 255 GLU GLU ILE ASN SER SER LEU VAL HET MG A 232 1 HET CL A 233 1 HET CL A 234 1 HET CL B 232 1 HET CL B 233 1 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION FORMUL 3 MG MG 2+ FORMUL 4 CL 4(CL 1-) FORMUL 8 HOH *593(H2 O) HELIX 1 1 ASN A 14 ASP A 23 1 10 HELIX 2 2 LYS A 24 ILE A 25 5 2 HELIX 3 3 ASP A 26 CYS A 30 5 5 HELIX 4 4 LYS A 36 ARG A 53 1 18 HELIX 5 5 ILE A 66 LEU A 80 1 15 HELIX 6 6 GLY A 92 GLU A 104 1 13 HELIX 7 7 PRO A 105 ARG A 110 5 6 HELIX 8 8 GLU A 123 ILE A 130 1 8 HELIX 9 9 ALA A 135 ALA A 150 1 16 HELIX 10 10 SER A 158 GLY A 170 1 13 HELIX 11 11 THR A 195 SER A 202 1 8 HELIX 12 12 GLY A 210 GLN A 215 1 6 HELIX 13 13 HIS A 218 LEU A 230 1 13 HELIX 14 14 ASN B 14 ASP B 23 1 10 HELIX 15 15 LYS B 36 ARG B 53 1 18 HELIX 16 16 ILE B 66 GLY B 81 1 16 HELIX 17 17 GLY B 92 GLU B 104 1 13 HELIX 18 18 PRO B 105 ARG B 110 5 6 HELIX 19 19 GLU B 123 ILE B 130 1 8 HELIX 20 20 ALA B 135 ALA B 150 1 16 HELIX 21 21 GLU B 161 GLY B 170 1 10 HELIX 22 22 THR B 195 GLY B 203 1 9 HELIX 23 23 GLY B 210 GLN B 215 1 6 HELIX 24 24 HIS B 218 LEU B 230 1 13 SHEET 1 A 9 VAL A 6 LEU A 10 0 SHEET 2 A 9 ARG A 31 GLY A 35 1 O ARG A 31 N VAL A 8 SHEET 3 A 9 VAL A 57 PHE A 63 1 O PHE A 58 N LEU A 32 SHEET 4 A 9 MET A 84 HIS A 88 1 O MET A 84 N LEU A 59 SHEET 5 A 9 LEU A 112 VAL A 116 1 O LEU A 112 N VAL A 85 SHEET 6 A 9 GLY A 154 VAL A 156 1 O GLY A 154 N GLY A 115 SHEET 7 A 9 LYS A 174 PRO A 178 1 O VAL A 176 N VAL A 155 SHEET 8 A 9 TYR A 206 ILE A 209 1 O TYR A 206 N THR A 177 SHEET 9 A 9 VAL A 6 LEU A 10 1 N ILE A 7 O LEU A 207 SHEET 1 B 9 VAL B 6 LEU B 10 0 SHEET 2 B 9 ARG B 31 GLY B 35 1 O ARG B 31 N VAL B 8 SHEET 3 B 9 VAL B 57 PHE B 63 1 O PHE B 58 N LEU B 32 SHEET 4 B 9 MET B 84 HIS B 88 1 O MET B 84 N LEU B 59 SHEET 5 B 9 LEU B 112 VAL B 116 1 O VAL B 116 N VAL B 87 SHEET 6 B 9 GLY B 154 VAL B 156 1 O GLY B 154 N GLY B 115 SHEET 7 B 9 LYS B 174 PRO B 178 1 O VAL B 176 N VAL B 155 SHEET 8 B 9 TYR B 206 ILE B 209 1 O TYR B 206 N THR B 177 SHEET 9 B 9 VAL B 6 LEU B 10 1 N ILE B 7 O LEU B 207 LINK OD1 ASP A 26 MG MG A 232 1555 1555 2.05 LINK MG MG A 232 O HOH A 330 1555 1555 2.19 LINK MG MG A 232 O HOH A 487 1555 1555 2.29 LINK MG MG A 232 O HOH A 516 1555 1555 2.12 SITE 1 AC1 4 ASP A 26 HOH A 330 HOH A 487 HOH A 516 SITE 1 AC2 2 PRO A 67 ASN A 68 SITE 1 AC3 4 ILE A 25 ASP A 26 THR A 29 GLU A 220 SITE 1 AC4 2 PRO B 67 ASN B 68 SITE 1 AC5 4 GLY B 107 LYS B 108 GLN B 128 HOH B 328 CRYST1 47.300 94.675 99.183 90.00 90.00 90.00 P 21 21 21 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021142 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010562 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010082 0.00000