HEADER TRANSFERASE/TRANSFERASE SUBSTRATE 26-SEP-11 3TYZ TITLE CRYSTAL STRUCTURE OF THE YERSINIA PESTIS DIHYDROPTEROATE SYNTHETASE TITLE 2 WITH SUBSTRATE TRANSITION STATE COMPLEX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 7,8-DIHYDROPTEROATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DIHYDROPTEROATE SYNTHASE; COMPND 5 EC: 2.5.1.15; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PESTIS; SOURCE 3 ORGANISM_TAXID: 632; SOURCE 4 STRAIN: KIM D27; SOURCE 5 GENE: DHPS, FOLP, Y0683, YPO3501, YP_0582; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS DIHYDROPTEROATE SYNTHASE, TRANSITION STATE COMPLEX, PABA, TIM BARREL, KEYWDS 2 TRANSFERASE-TRANSFERASE SUBSTRATE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.WU REVDAT 2 28-FEB-24 3TYZ 1 REMARK SEQADV LINK REVDAT 1 14-MAR-12 3TYZ 0 JRNL AUTH M.K.YUN,Y.WU,Z.LI,Y.ZHAO,M.B.WADDELL,A.M.FERREIRA,R.E.LEE, JRNL AUTH 2 D.BASHFORD,S.W.WHITE JRNL TITL CATALYSIS AND SULFA DRUG RESISTANCE IN DIHYDROPTEROATE JRNL TITL 2 SYNTHASE. JRNL REF SCIENCE V. 335 1110 2012 JRNL REFN ISSN 0036-8075 JRNL PMID 22383850 JRNL DOI 10.1126/SCIENCE.1214641 REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 31894 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1606 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) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2108 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4123 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 255 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.24000 REMARK 3 B22 (A**2) : 0.89000 REMARK 3 B33 (A**2) : 0.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.46000 REMARK 3 B23 (A**2) : 0.00000 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): 0.186 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.137 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.201 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4285 ; 0.008 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5831 ; 1.144 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 559 ; 5.107 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 183 ;39.198 ;24.536 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 692 ;13.815 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;14.157 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 668 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3253 ; 0.004 ; 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): 2756 ; 0.285 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4408 ; 0.520 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1529 ; 1.027 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1418 ; 1.621 ; 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 : 4 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 1 A 275 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6531 18.7238 39.6697 REMARK 3 T TENSOR REMARK 3 T11: 0.0400 T22: 0.0202 REMARK 3 T33: 0.0828 T12: 0.0037 REMARK 3 T13: 0.0106 T23: 0.0174 REMARK 3 L TENSOR REMARK 3 L11: 1.7684 L22: 1.2161 REMARK 3 L33: 1.5096 L12: 0.0604 REMARK 3 L13: 0.4744 L23: 0.6959 REMARK 3 S TENSOR REMARK 3 S11: 0.0103 S12: -0.1445 S13: 0.0967 REMARK 3 S21: 0.1343 S22: -0.0246 S23: -0.0516 REMARK 3 S31: -0.0652 S32: -0.0538 S33: 0.0143 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 : B 1 B 276 REMARK 3 ORIGIN FOR THE GROUP (A): 16.2956 -1.9148 7.1013 REMARK 3 T TENSOR REMARK 3 T11: 0.1384 T22: 0.2046 REMARK 3 T33: 0.1286 T12: -0.0033 REMARK 3 T13: -0.0179 T23: 0.0012 REMARK 3 L TENSOR REMARK 3 L11: 0.9461 L22: 1.0223 REMARK 3 L33: 2.4086 L12: 0.1096 REMARK 3 L13: -0.0479 L23: 0.7011 REMARK 3 S TENSOR REMARK 3 S11: 0.0332 S12: 0.3544 S13: -0.1728 REMARK 3 S21: -0.2208 S22: 0.0136 S23: 0.0231 REMARK 3 S31: 0.2247 S32: -0.1928 S33: -0.0468 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 281 A 281 REMARK 3 ORIGIN FOR THE GROUP (A): 13.1307 13.8079 42.3851 REMARK 3 T TENSOR REMARK 3 T11: 0.1323 T22: 0.1862 REMARK 3 T33: 0.2146 T12: 0.0044 REMARK 3 T13: 0.0496 T23: 0.0150 REMARK 3 L TENSOR REMARK 3 L11: 1.2281 L22: 6.8706 REMARK 3 L33: 0.1608 L12: 2.9032 REMARK 3 L13: -0.4442 L23: -1.0506 REMARK 3 S TENSOR REMARK 3 S11: 0.2733 S12: -0.1618 S13: 0.2131 REMARK 3 S21: 0.4361 S22: -0.2764 S23: 0.4940 REMARK 3 S31: -0.0684 S32: 0.0548 S33: 0.0032 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 : B 281 B 281 REMARK 3 ORIGIN FOR THE GROUP (A): 23.3046 -3.5407 7.9815 REMARK 3 T TENSOR REMARK 3 T11: 0.2016 T22: 0.2416 REMARK 3 T33: 0.1626 T12: 0.0655 REMARK 3 T13: -0.0459 T23: -0.0605 REMARK 3 L TENSOR REMARK 3 L11: 3.1291 L22: 3.4006 REMARK 3 L33: 1.1989 L12: 0.2795 REMARK 3 L13: -1.7993 L23: -0.8997 REMARK 3 S TENSOR REMARK 3 S11: 0.0326 S12: 0.7078 S13: -0.2615 REMARK 3 S21: -0.3104 S22: -0.1880 S23: -0.2748 REMARK 3 S31: 0.0453 S32: -0.3535 S33: 0.1554 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 U VALUES : RESIDUAL ONLY REMARK 4 REMARK 4 3TYZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068096. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-APR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6-7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97954 REMARK 200 MONOCHROMATOR : SI-220 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31898 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.29300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 20,000, MES(PH6.5), PH 6-7, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 25.26100 REMARK 290 SMTRY3 2 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: 3960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 LYS A 276 REMARK 465 GLY A 277 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 GLY B 277 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 146 CG CD CE NZ REMARK 470 LEU B 8 CG CD1 CD2 REMARK 470 THR B 9 OG1 CG2 REMARK 470 SER B 70 OG REMARK 470 GLU B 71 CG CD OE1 OE2 REMARK 470 GLN B 72 CG CD OE1 NE2 REMARK 470 VAL B 78 CG1 CG2 REMARK 470 GLN B 87 CG CD OE1 NE2 REMARK 470 ARG B 88 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 102 CG1 CG2 REMARK 470 GLU B 105 CG CD OE1 OE2 REMARK 470 SER B 106 OG REMARK 470 HIS B 108 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 131 CG CD CE NZ REMARK 470 LYS B 146 CG CD CE NZ REMARK 470 LYS B 179 CG CD CE NZ REMARK 470 LYS B 181 CG CD CE NZ 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 330 O HOH A 366 1.86 REMARK 500 O HIS A 150 O HOH A 413 1.87 REMARK 500 O HOH A 430 O HOH A 466 1.96 REMARK 500 O HOH A 387 O HOH A 388 2.01 REMARK 500 O HOH A 364 O HOH A 365 2.13 REMARK 500 O HOH A 411 O HOH A 417 2.16 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 A 378 O HOH A 397 2556 1.69 REMARK 500 O HOH A 408 O HOH A 419 2556 1.98 REMARK 500 O HOH A 433 O HOH A 441 2556 2.00 REMARK 500 O HOH A 410 O HOH A 417 2556 2.11 REMARK 500 O HOH A 427 O HOH B 344 2656 2.16 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 ALA A 5 118.77 -167.31 REMARK 500 VAL A 23 51.38 -111.95 REMARK 500 ASP A 30 23.84 -140.83 REMARK 500 SER A 151 62.65 39.42 REMARK 500 ARG A 220 12.02 59.91 REMARK 500 HIS B 2 109.10 -160.07 REMARK 500 VAL B 23 57.30 -106.31 REMARK 500 ASP B 30 17.50 -151.92 REMARK 500 SER B 151 71.87 42.90 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 281 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 22 OD1 REMARK 620 2 POP A 279 O2 106.2 REMARK 620 3 POP A 279 O5 94.5 81.8 REMARK 620 4 HOH A 305 O 91.2 162.5 94.8 REMARK 620 5 HOH A 306 O 90.8 95.7 174.5 86.1 REMARK 620 6 HOH A 307 O 173.2 80.6 86.0 82.0 88.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 281 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 22 OD1 REMARK 620 2 POP B 279 O2 92.8 REMARK 620 3 POP B 279 O5 93.5 86.3 REMARK 620 4 HOH B 282 O 88.8 176.8 90.8 REMARK 620 5 HOH B 283 O 169.1 98.0 88.8 80.6 REMARK 620 6 HOH B 284 O 89.8 101.3 171.5 81.5 86.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XHP A 278 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP A 279 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PAB A 280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 281 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XHP B 278 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE POP B 279 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PAB B 280 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 281 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TYU RELATED DB: PDB REMARK 900 RELATED ID: 3TZF RELATED DB: PDB REMARK 900 RELATED ID: 3TZN RELATED DB: PDB DBREF 3TYZ A 1 277 UNP Q7CKJ1 Q7CKJ1_YERPE 1 277 DBREF 3TYZ B 1 277 UNP Q7CKJ1 Q7CKJ1_YERPE 1 277 SEQADV 3TYZ GLY A -2 UNP Q7CKJ1 EXPRESSION TAG SEQADV 3TYZ SER A -1 UNP Q7CKJ1 EXPRESSION TAG SEQADV 3TYZ HIS A 0 UNP Q7CKJ1 EXPRESSION TAG SEQADV 3TYZ GLY B -2 UNP Q7CKJ1 EXPRESSION TAG SEQADV 3TYZ SER B -1 UNP Q7CKJ1 EXPRESSION TAG SEQADV 3TYZ HIS B 0 UNP Q7CKJ1 EXPRESSION TAG SEQRES 1 A 280 GLY SER HIS MET HIS LEU THR ALA ARG GLY LEU THR LEU SEQRES 2 A 280 ASP LEU SER ARG PRO GLN VAL MET GLY ILE LEU ASN VAL SEQRES 3 A 280 THR PRO ASP SER PHE SER ASP GLY GLY CYS HIS ASN ASN SEQRES 4 A 280 LEU ASP GLN ALA LEU GLN HIS ALA GLN ARG MET LEU SER SEQRES 5 A 280 ALA GLY ALA THR LEU ILE ASP ILE GLY GLY GLU SER THR SEQRES 6 A 280 ARG PRO GLY ALA ALA GLU VAL SER GLU GLN GLU GLU LEU SEQRES 7 A 280 ASP ARG VAL VAL PRO VAL VAL GLU ALA LEU ALA GLN ARG SEQRES 8 A 280 PHE ASP VAL TRP LEU SER VAL ASP THR SER LYS ALA ALA SEQRES 9 A 280 VAL ILE THR GLU SER ALA HIS ALA GLY ALA HIS LEU ILE SEQRES 10 A 280 ASN ASP ILE ARG SER LEU GLN GLU PRO GLY ALA LEU GLU SEQRES 11 A 280 ALA ALA ALA LYS THR GLY LEU PRO VAL CYS LEU MET HIS SEQRES 12 A 280 MET GLN GLY GLN PRO LYS ASN MET GLN HIS SER PRO TYR SEQRES 13 A 280 TYR ASP ASP LEU MET THR ASP ILE ASN ARG PHE PHE GLN SEQRES 14 A 280 HIS HIS ILE GLU ARG CYS VAL ALA ALA GLY ILE ALA LYS SEQRES 15 A 280 ASN LYS LEU LEU LEU ASP PRO GLY PHE GLY PHE GLY LYS SEQRES 16 A 280 ASN LEU ALA HIS ASN TYR GLN LEU LEU ALA HIS LEU SER SEQRES 17 A 280 GLU LEU HIS HIS PHE GLU LEU PRO LEU LEU VAL GLY MET SEQRES 18 A 280 SER ARG LYS SER MET VAL GLY GLN LEU LEU ASN VAL PRO SEQRES 19 A 280 PRO GLN GLN ARG VAL ILE GLY SER VAL ALA CYS ALA VAL SEQRES 20 A 280 ILE ALA ALA MET GLN GLY ALA GLN ILE ILE ARG VAL HIS SEQRES 21 A 280 ASP VAL LYS GLU THR VAL GLU ALA MET CYS ILE VAL GLU SEQRES 22 A 280 ALA THR ARG SER ALA LYS GLY SEQRES 1 B 280 GLY SER HIS MET HIS LEU THR ALA ARG GLY LEU THR LEU SEQRES 2 B 280 ASP LEU SER ARG PRO GLN VAL MET GLY ILE LEU ASN VAL SEQRES 3 B 280 THR PRO ASP SER PHE SER ASP GLY GLY CYS HIS ASN ASN SEQRES 4 B 280 LEU ASP GLN ALA LEU GLN HIS ALA GLN ARG MET LEU SER SEQRES 5 B 280 ALA GLY ALA THR LEU ILE ASP ILE GLY GLY GLU SER THR SEQRES 6 B 280 ARG PRO GLY ALA ALA GLU VAL SER GLU GLN GLU GLU LEU SEQRES 7 B 280 ASP ARG VAL VAL PRO VAL VAL GLU ALA LEU ALA GLN ARG SEQRES 8 B 280 PHE ASP VAL TRP LEU SER VAL ASP THR SER LYS ALA ALA SEQRES 9 B 280 VAL ILE THR GLU SER ALA HIS ALA GLY ALA HIS LEU ILE SEQRES 10 B 280 ASN ASP ILE ARG SER LEU GLN GLU PRO GLY ALA LEU GLU SEQRES 11 B 280 ALA ALA ALA LYS THR GLY LEU PRO VAL CYS LEU MET HIS SEQRES 12 B 280 MET GLN GLY GLN PRO LYS ASN MET GLN HIS SER PRO TYR SEQRES 13 B 280 TYR ASP ASP LEU MET THR ASP ILE ASN ARG PHE PHE GLN SEQRES 14 B 280 HIS HIS ILE GLU ARG CYS VAL ALA ALA GLY ILE ALA LYS SEQRES 15 B 280 ASN LYS LEU LEU LEU ASP PRO GLY PHE GLY PHE GLY LYS SEQRES 16 B 280 ASN LEU ALA HIS ASN TYR GLN LEU LEU ALA HIS LEU SER SEQRES 17 B 280 GLU LEU HIS HIS PHE GLU LEU PRO LEU LEU VAL GLY MET SEQRES 18 B 280 SER ARG LYS SER MET VAL GLY GLN LEU LEU ASN VAL PRO SEQRES 19 B 280 PRO GLN GLN ARG VAL ILE GLY SER VAL ALA CYS ALA VAL SEQRES 20 B 280 ILE ALA ALA MET GLN GLY ALA GLN ILE ILE ARG VAL HIS SEQRES 21 B 280 ASP VAL LYS GLU THR VAL GLU ALA MET CYS ILE VAL GLU SEQRES 22 B 280 ALA THR ARG SER ALA LYS GLY HET XHP A 278 13 HET POP A 279 9 HET PAB A 280 10 HET MG A 281 1 HET XHP B 278 13 HET POP B 279 9 HET PAB B 280 10 HET MG B 281 1 HETNAM XHP 2-AMINO-6-METHYLIDENE-6,7-DIHYDROPTERIDIN-4(3H)-ONE HETNAM POP PYROPHOSPHATE 2- HETNAM PAB 4-AMINOBENZOIC ACID HETNAM MG MAGNESIUM ION FORMUL 3 XHP 2(C7 H7 N5 O) FORMUL 4 POP 2(H2 O7 P2 2-) FORMUL 5 PAB 2(C7 H7 N O2) FORMUL 6 MG 2(MG 2+) FORMUL 11 HOH *255(H2 O) HELIX 1 1 ASN A 36 GLY A 51 1 16 HELIX 2 2 SER A 70 PHE A 89 1 20 HELIX 3 3 LYS A 99 ALA A 109 1 11 HELIX 4 4 GLY A 124 GLY A 133 1 10 HELIX 5 5 ASP A 156 ALA A 175 1 20 HELIX 6 6 ALA A 178 ASN A 180 5 3 HELIX 7 7 ASN A 193 HIS A 203 1 11 HELIX 8 8 LEU A 204 GLU A 211 5 8 HELIX 9 9 LYS A 221 ASN A 229 1 9 HELIX 10 10 PRO A 231 GLN A 234 5 4 HELIX 11 11 ARG A 235 GLN A 249 1 15 HELIX 12 12 ASP A 258 SER A 274 1 17 HELIX 13 13 ASN B 36 ALA B 50 1 15 HELIX 14 14 SER B 70 GLN B 87 1 18 HELIX 15 15 LYS B 99 ALA B 109 1 11 HELIX 16 16 GLY B 124 GLY B 133 1 10 HELIX 17 17 ASP B 156 ALA B 175 1 20 HELIX 18 18 ALA B 178 ASN B 180 5 3 HELIX 19 19 ASN B 193 HIS B 203 1 11 HELIX 20 20 LEU B 204 GLU B 211 5 8 HELIX 21 21 LYS B 221 ASN B 229 1 9 HELIX 22 22 PRO B 231 GLN B 234 5 4 HELIX 23 23 ARG B 235 GLN B 249 1 15 HELIX 24 24 ASP B 258 SER B 274 1 17 SHEET 1 A 2 HIS A 2 ALA A 5 0 SHEET 2 A 2 LEU A 8 ASP A 11 -1 O LEU A 8 N ALA A 5 SHEET 1 B 8 LEU A 182 ASP A 185 0 SHEET 2 B 8 VAL A 136 MET A 139 1 N LEU A 138 O LEU A 183 SHEET 3 B 8 LEU A 113 ASP A 116 1 N ILE A 114 O CYS A 137 SHEET 4 B 8 TRP A 92 ASP A 96 1 N VAL A 95 O LEU A 113 SHEET 5 B 8 LEU A 54 GLY A 58 1 N ILE A 57 O SER A 94 SHEET 6 B 8 GLN A 16 ASN A 22 1 N LEU A 21 O ASP A 56 SHEET 7 B 8 ILE A 253 VAL A 256 1 O ILE A 254 N GLN A 16 SHEET 8 B 8 LEU A 215 VAL A 216 1 N VAL A 216 O ARG A 255 SHEET 1 C 2 HIS B 2 ALA B 5 0 SHEET 2 C 2 LEU B 8 ASP B 11 -1 O LEU B 10 N LEU B 3 SHEET 1 D 8 LEU B 182 ASP B 185 0 SHEET 2 D 8 VAL B 136 MET B 139 1 N LEU B 138 O LEU B 183 SHEET 3 D 8 LEU B 113 ASP B 116 1 N ILE B 114 O CYS B 137 SHEET 4 D 8 TRP B 92 ASP B 96 1 N VAL B 95 O ASN B 115 SHEET 5 D 8 LEU B 54 GLY B 58 1 N ILE B 57 O ASP B 96 SHEET 6 D 8 GLN B 16 ASN B 22 1 N GLY B 19 O ASP B 56 SHEET 7 D 8 ILE B 253 VAL B 256 1 O ILE B 254 N MET B 18 SHEET 8 D 8 LEU B 215 VAL B 216 1 N VAL B 216 O ARG B 255 LINK OD1 ASN A 22 MG MG A 281 1555 1555 2.08 LINK O2 POP A 279 MG MG A 281 1555 1555 2.06 LINK O5 POP A 279 MG MG A 281 1555 1555 2.18 LINK MG MG A 281 O HOH A 305 1555 1555 2.08 LINK MG MG A 281 O HOH A 306 1555 1555 2.22 LINK MG MG A 281 O HOH A 307 1555 1555 2.17 LINK OD1 ASN B 22 MG MG B 281 1555 1555 2.11 LINK O2 POP B 279 MG MG B 281 1555 1555 1.99 LINK O5 POP B 279 MG MG B 281 1555 1555 2.05 LINK MG MG B 281 O HOH B 282 1555 1555 2.45 LINK MG MG B 281 O HOH B 283 1555 1555 2.12 LINK MG MG B 281 O HOH B 284 1555 1555 2.04 SITE 1 AC1 12 ASP A 96 ASN A 115 ILE A 117 ASP A 185 SITE 2 AC1 12 PHE A 190 LEU A 215 GLY A 217 LYS A 221 SITE 3 AC1 12 ARG A 255 POP A 279 PAB A 280 HOH A 352 SITE 1 AC2 14 ASN A 22 SER A 27 PHE A 28 SER A 61 SITE 2 AC2 14 THR A 62 ARG A 63 ARG A 255 HIS A 257 SITE 3 AC2 14 XHP A 278 PAB A 280 MG A 281 HOH A 303 SITE 4 AC2 14 HOH A 307 HOH A 322 SITE 1 AC3 11 PHE A 28 THR A 62 ARG A 63 PHE A 190 SITE 2 AC3 11 LYS A 221 SER A 222 XHP A 278 POP A 279 SITE 3 AC3 11 HOH A 289 HOH A 290 HOH A 320 SITE 1 AC4 6 ASN A 22 SER A 27 POP A 279 HOH A 305 SITE 2 AC4 6 HOH A 306 HOH A 307 SITE 1 AC5 14 ASP B 96 ASN B 115 ILE B 117 MET B 139 SITE 2 AC5 14 ASP B 185 PHE B 190 LEU B 215 GLY B 217 SITE 3 AC5 14 LYS B 221 ARG B 255 POP B 279 PAB B 280 SITE 4 AC5 14 HOH B 283 HOH B 295 SITE 1 AC6 14 ASN B 22 SER B 27 PHE B 28 SER B 61 SITE 2 AC6 14 THR B 62 ARG B 63 ARG B 255 HIS B 257 SITE 3 AC6 14 XHP B 278 PAB B 280 MG B 281 HOH B 283 SITE 4 AC6 14 HOH B 287 HOH B 303 SITE 1 AC7 11 PHE B 28 THR B 62 ARG B 63 GLY B 189 SITE 2 AC7 11 PHE B 190 LYS B 221 SER B 222 XHP B 278 SITE 3 AC7 11 POP B 279 HOH B 292 HOH B 293 SITE 1 AC8 5 ASN B 22 POP B 279 HOH B 282 HOH B 283 SITE 2 AC8 5 HOH B 284 CRYST1 70.179 50.522 74.668 90.00 90.75 90.00 P 1 21 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014249 0.000000 0.000185 0.00000 SCALE2 0.000000 0.019793 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013394 0.00000