HEADER HYDROLASE 15-JUN-18 6DT3 TITLE 1.2 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF NUCLEOSIDE TRIPHOSPHATASE TITLE 2 NUDI FROM KLEBSIELLA PNEUMONIAE IN COMPLEX WITH HEPES COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE TRIPHOSPHATASE NUDI; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NUCLEOTIDE DIPHOSPHATASE NUDI, PYRIMIDINE DEOXYNUCLEOSIDE COMPND 5 TRIPHOSPHATE DIPHOSPHATASE, DCTP DIPHOSPHATASE, DTTP DIPHOSPHATASE, COMPND 6 DUTP DIPHOSPHATASE; COMPND 7 EC: 3.6.1.9,3.6.1.12,3.6.1.-,3.6.1.23; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: KLEBSIELLA PNEUMONIAE SUBSP. PNEUMONIAE NTUH- SOURCE 3 K2044; SOURCE 4 ORGANISM_TAXID: 484021; SOURCE 5 GENE: NUDI, B1727_21840; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 GOLD; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG68 KEYWDS STRUCTURAL GENOMICS, CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS KEYWDS 2 DISEASES, CSGID, PUTATIVE NUDIX HYDROLASE, HEPES, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.MINASOV,L.SHUVALOVA,S.PSHENYCHNYI,M.ENDRES,K.J.F.SATCHELL, AUTHOR 2 A.JOACHIMIAK,CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES AUTHOR 3 (CSGID) REVDAT 3 23-OCT-24 6DT3 1 REMARK REVDAT 2 14-JUN-23 6DT3 1 JRNL REVDAT 1 27-JUN-18 6DT3 0 JRNL AUTH N.L.INNISS,T.J.KOCHAN,G.MINASOV,Z.WAWRZAK,C.CHANG,K.TAN, JRNL AUTH 2 L.SHUVALOVA,O.KIRYUKHINA,S.PSHENYCHNYI,R.WU,I.DUBROVSKA, JRNL AUTH 3 G.BABNIGG,M.ENDRES,W.F.ANDERSON,A.R.HAUSER,A.JOACHIMIAK, JRNL AUTH 4 K.J.F.SATCHELL JRNL TITL A STRUCTURAL SYSTEMS BIOLOGY APPROACH TO HIGH-RISK CG23 JRNL TITL 2 KLEBSIELLA PNEUMONIAE. JRNL REF MICROBIOL RESOUR ANNOUNC V. 12 01322 2023 JRNL REFN ISSN 2576-098X JRNL PMID 36695589 JRNL DOI 10.1128/MRA.01013-22 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 74887 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) : 0.153 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3897 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5395 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 297 REMARK 3 BIN FREE R VALUE : 0.2500 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2312 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 343 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : 0.66000 REMARK 3 B33 (A**2) : -0.68000 REMARK 3 B12 (A**2) : 0.61000 REMARK 3 B13 (A**2) : -0.47000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.047 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.046 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.036 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.771 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2618 ; 0.008 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 2325 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3574 ; 1.400 ; 1.687 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5478 ; 0.505 ; 1.689 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 332 ; 5.562 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;27.156 ;21.274 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 439 ;10.458 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;10.724 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 336 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3071 ; 0.040 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 485 ; 0.037 ; 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): 1271 ; 1.380 ; 1.051 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1270 ; 1.374 ; 1.049 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1622 ; 1.614 ; 1.582 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1623 ; 1.614 ; 1.584 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1347 ; 2.000 ; 1.380 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1347 ; 1.985 ; 1.380 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1953 ; 2.288 ; 1.969 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2950 ; 2.807 ;14.602 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2951 ; 2.806 ;14.606 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4943 ;11.074 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 190 ;16.896 ;10.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5039 ; 7.487 ;10.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 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 -1 A 24 REMARK 3 ORIGIN FOR THE GROUP (A): 30.8761 8.4863 21.7907 REMARK 3 T TENSOR REMARK 3 T11: 0.0672 T22: 0.0180 REMARK 3 T33: 0.0624 T12: -0.0164 REMARK 3 T13: 0.0177 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 0.6153 L22: 0.0050 REMARK 3 L33: 1.6171 L12: -0.0258 REMARK 3 L13: -0.1019 L23: -0.0638 REMARK 3 S TENSOR REMARK 3 S11: -0.0167 S12: -0.0851 S13: -0.0656 REMARK 3 S21: 0.0023 S22: 0.0064 S23: 0.0104 REMARK 3 S31: -0.0068 S32: -0.0138 S33: 0.0103 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 25 A 75 REMARK 3 ORIGIN FOR THE GROUP (A): 25.7199 8.4817 21.6132 REMARK 3 T TENSOR REMARK 3 T11: 0.0326 T22: 0.0266 REMARK 3 T33: 0.0276 T12: -0.0018 REMARK 3 T13: 0.0092 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 0.7839 L22: 0.3247 REMARK 3 L33: 0.9516 L12: 0.0059 REMARK 3 L13: 0.0129 L23: -0.2395 REMARK 3 S TENSOR REMARK 3 S11: 0.0128 S12: -0.1129 S13: -0.0355 REMARK 3 S21: 0.0105 S22: 0.0212 S23: 0.0073 REMARK 3 S31: 0.0442 S32: -0.0961 S33: -0.0340 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 76 A 88 REMARK 3 ORIGIN FOR THE GROUP (A): 38.8675 -5.8436 9.6754 REMARK 3 T TENSOR REMARK 3 T11: 0.0635 T22: 0.0255 REMARK 3 T33: 0.1191 T12: -0.0216 REMARK 3 T13: -0.0121 T23: -0.0070 REMARK 3 L TENSOR REMARK 3 L11: 0.6949 L22: 11.6068 REMARK 3 L33: 0.5433 L12: -1.8405 REMARK 3 L13: 0.1445 L23: -0.3065 REMARK 3 S TENSOR REMARK 3 S11: 0.0110 S12: -0.0194 S13: -0.1609 REMARK 3 S21: 0.3935 S22: -0.0791 S23: -0.0616 REMARK 3 S31: 0.0966 S32: -0.1097 S33: 0.0681 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 89 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): 33.3613 12.5077 25.7536 REMARK 3 T TENSOR REMARK 3 T11: 0.0430 T22: 0.0254 REMARK 3 T33: 0.0290 T12: -0.0082 REMARK 3 T13: 0.0124 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 0.4973 L22: 0.2737 REMARK 3 L33: 1.5973 L12: 0.0759 REMARK 3 L13: 0.0473 L23: -0.2086 REMARK 3 S TENSOR REMARK 3 S11: 0.0364 S12: -0.1057 S13: 0.0217 REMARK 3 S21: 0.0701 S22: -0.0247 S23: -0.0211 REMARK 3 S31: -0.0762 S32: 0.0538 S33: -0.0117 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 13 REMARK 3 ORIGIN FOR THE GROUP (A): 22.3722 15.4963 1.6306 REMARK 3 T TENSOR REMARK 3 T11: 0.0214 T22: 0.0120 REMARK 3 T33: 0.0243 T12: 0.0021 REMARK 3 T13: 0.0017 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 3.0749 L22: 3.2856 REMARK 3 L33: 0.7526 L12: 2.6540 REMARK 3 L13: -1.2404 L23: -1.4319 REMARK 3 S TENSOR REMARK 3 S11: -0.0525 S12: 0.0596 S13: -0.0652 REMARK 3 S21: -0.0845 S22: -0.0013 S23: -0.0666 REMARK 3 S31: 0.0123 S32: -0.0334 S33: 0.0538 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 14 B 39 REMARK 3 ORIGIN FOR THE GROUP (A): 20.3367 25.7872 -6.6064 REMARK 3 T TENSOR REMARK 3 T11: 0.0089 T22: 0.0275 REMARK 3 T33: 0.0256 T12: 0.0058 REMARK 3 T13: 0.0089 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 1.3802 L22: 2.3017 REMARK 3 L33: 1.6606 L12: 0.4262 REMARK 3 L13: 0.0678 L23: -0.1572 REMARK 3 S TENSOR REMARK 3 S11: 0.0433 S12: 0.0854 S13: 0.0318 REMARK 3 S21: 0.0557 S22: 0.0097 S23: 0.0416 REMARK 3 S31: 0.0130 S32: -0.1620 S33: -0.0530 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 40 B 61 REMARK 3 ORIGIN FOR THE GROUP (A): 32.6082 14.7869 -5.3293 REMARK 3 T TENSOR REMARK 3 T11: 0.0172 T22: 0.0108 REMARK 3 T33: 0.0321 T12: 0.0065 REMARK 3 T13: -0.0035 T23: -0.0040 REMARK 3 L TENSOR REMARK 3 L11: 1.3396 L22: 2.1975 REMARK 3 L33: 3.6470 L12: -0.7976 REMARK 3 L13: 0.4912 L23: -1.8739 REMARK 3 S TENSOR REMARK 3 S11: 0.0992 S12: 0.1082 S13: -0.0796 REMARK 3 S21: -0.1047 S22: -0.0083 S23: 0.0593 REMARK 3 S31: 0.1329 S32: -0.0063 S33: -0.0909 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 62 B 141 REMARK 3 ORIGIN FOR THE GROUP (A): 22.9702 24.4334 -1.6586 REMARK 3 T TENSOR REMARK 3 T11: 0.0149 T22: 0.0117 REMARK 3 T33: 0.0332 T12: 0.0093 REMARK 3 T13: 0.0065 T23: 0.0041 REMARK 3 L TENSOR REMARK 3 L11: 0.5539 L22: 0.5341 REMARK 3 L33: 0.7216 L12: 0.0879 REMARK 3 L13: -0.0827 L23: -0.2324 REMARK 3 S TENSOR REMARK 3 S11: 0.0029 S12: 0.0476 S13: 0.0517 REMARK 3 S21: -0.0057 S22: -0.0198 S23: -0.0108 REMARK 3 S31: -0.0527 S32: -0.0430 S33: 0.0169 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6DT3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000235199. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : C(111) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 78810 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 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 (%) : 92.3 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : 0.07000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.79000 REMARK 200 R SYM FOR SHELL (I) : 0.79000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10.0 MG/ML PROTEIN, 0.5 M SODIUM REMARK 280 CHLORIDE, 0.01 M TRIS, PH 8.3 AGAINST CLASSICS II (F8) (0.2 M REMARK 280 AMMONIUM SULFATE, 0.1 M HEPES, PH 7.5, 25% W/V PEG3350), VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 2390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 SER A -2 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 TRP A 70 -71.43 -119.33 REMARK 500 TRP B 70 -67.82 -123.62 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 B 466 DISTANCE = 6.69 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: CSGID-IDP96903 RELATED DB: TARGETTRACK DBREF1 6DT3 A 1 141 UNP A0A1W1Q5B1_KLEPN DBREF2 6DT3 A A0A1W1Q5B1 1 141 DBREF1 6DT3 B 1 141 UNP A0A1W1Q5B1_KLEPN DBREF2 6DT3 B A0A1W1Q5B1 1 141 SEQADV 6DT3 SER A -2 UNP A0A1W1Q5B EXPRESSION TAG SEQADV 6DT3 ASN A -1 UNP A0A1W1Q5B EXPRESSION TAG SEQADV 6DT3 ALA A 0 UNP A0A1W1Q5B EXPRESSION TAG SEQADV 6DT3 GLN A 3 UNP A0A1W1Q5B HIS 3 CONFLICT SEQADV 6DT3 SER B -2 UNP A0A1W1Q5B EXPRESSION TAG SEQADV 6DT3 ASN B -1 UNP A0A1W1Q5B EXPRESSION TAG SEQADV 6DT3 ALA B 0 UNP A0A1W1Q5B EXPRESSION TAG SEQADV 6DT3 GLN B 3 UNP A0A1W1Q5B HIS 3 CONFLICT SEQRES 1 A 144 SER ASN ALA MSE ARG GLN ARG THR ILE VAL CYS PRO LEU SEQRES 2 A 144 ILE GLU ASN GLU GLY HIS TYR LEU LEU CYS LYS MSE ALA SEQRES 3 A 144 ALA ASP ARG GLY VAL PHE PRO GLY GLN TRP ALA LEU SER SEQRES 4 A 144 GLY GLY GLY VAL GLU PRO GLY GLU ARG ILE GLU GLU ALA SEQRES 5 A 144 LEU ARG ARG GLU ILE ARG GLU GLU LEU GLY GLU LYS LEU SEQRES 6 A 144 ILE LEU THR HIS ILE ALA PRO TRP CYS PHE ARG ASP ASP SEQRES 7 A 144 THR ARG VAL LYS THR TYR PRO ASP GLY HIS GLN GLU THR SEQRES 8 A 144 ILE TYR MSE ILE TYR LEU ILE PHE ASN CYS VAL SER ALA SEQRES 9 A 144 ASN ARG ASP VAL THR ILE ASN GLU GLU PHE ASP ASP TYR SEQRES 10 A 144 ALA TRP VAL LYS ALA GLU ASP LEU LYS ASN TYR ASP LEU SEQRES 11 A 144 ASN ALA ALA THR ARG VAL THR LEU SER LEU LYS GLY LEU SEQRES 12 A 144 LEU SEQRES 1 B 144 SER ASN ALA MSE ARG GLN ARG THR ILE VAL CYS PRO LEU SEQRES 2 B 144 ILE GLU ASN GLU GLY HIS TYR LEU LEU CYS LYS MSE ALA SEQRES 3 B 144 ALA ASP ARG GLY VAL PHE PRO GLY GLN TRP ALA LEU SER SEQRES 4 B 144 GLY GLY GLY VAL GLU PRO GLY GLU ARG ILE GLU GLU ALA SEQRES 5 B 144 LEU ARG ARG GLU ILE ARG GLU GLU LEU GLY GLU LYS LEU SEQRES 6 B 144 ILE LEU THR HIS ILE ALA PRO TRP CYS PHE ARG ASP ASP SEQRES 7 B 144 THR ARG VAL LYS THR TYR PRO ASP GLY HIS GLN GLU THR SEQRES 8 B 144 ILE TYR MSE ILE TYR LEU ILE PHE ASN CYS VAL SER ALA SEQRES 9 B 144 ASN ARG ASP VAL THR ILE ASN GLU GLU PHE ASP ASP TYR SEQRES 10 B 144 ALA TRP VAL LYS ALA GLU ASP LEU LYS ASN TYR ASP LEU SEQRES 11 B 144 ASN ALA ALA THR ARG VAL THR LEU SER LEU LYS GLY LEU SEQRES 12 B 144 LEU MODRES 6DT3 MSE A 1 MET MODIFIED RESIDUE MODRES 6DT3 MSE A 22 MET MODIFIED RESIDUE MODRES 6DT3 MSE A 91 MET MODIFIED RESIDUE MODRES 6DT3 MSE B 1 MET MODIFIED RESIDUE MODRES 6DT3 MSE B 22 MET MODIFIED RESIDUE MODRES 6DT3 MSE B 91 MET MODIFIED RESIDUE HET MSE A 1 16 HET MSE A 22 8 HET MSE A 91 16 HET MSE B 1 16 HET MSE B 22 16 HET MSE B 91 8 HET EPE B 201 15 HETNAM MSE SELENOMETHIONINE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 EPE C8 H18 N2 O4 S FORMUL 4 HOH *343(H2 O) HELIX 1 AA1 ARG A 45 GLY A 59 1 15 HELIX 2 AA2 GLU A 120 TYR A 125 5 6 HELIX 3 AA3 ASN A 128 LYS A 138 1 11 HELIX 4 AA4 ARG B 45 GLY B 59 1 15 HELIX 5 AA5 GLU B 120 TYR B 125 5 6 HELIX 6 AA6 ASN B 128 LYS B 138 1 11 SHEET 1 AA1 5 TRP A 33 ALA A 34 0 SHEET 2 AA1 5 HIS A 16 MSE A 22 -1 N CYS A 20 O ALA A 34 SHEET 3 AA1 5 ALA A 0 ASN A 13 -1 N ASN A 13 O HIS A 16 SHEET 4 AA1 5 GLN A 86 SER A 100 1 O ILE A 92 N ILE A 6 SHEET 5 AA1 5 LEU A 64 THR A 80 -1 N ARG A 77 O ILE A 89 SHEET 1 AA2 4 GLY A 38 GLY A 39 0 SHEET 2 AA2 4 ALA A 0 ASN A 13 -1 N VAL A 7 O GLY A 38 SHEET 3 AA2 4 HIS A 16 MSE A 22 -1 O HIS A 16 N ASN A 13 SHEET 4 AA2 4 PHE A 111 LYS A 118 -1 O VAL A 117 N TYR A 17 SHEET 1 AA3 5 TRP B 33 ALA B 34 0 SHEET 2 AA3 5 HIS B 16 MSE B 22 -1 N CYS B 20 O ALA B 34 SHEET 3 AA3 5 ARG B 2 ASN B 13 -1 N ASN B 13 O HIS B 16 SHEET 4 AA3 5 GLN B 86 SER B 100 1 O TYR B 90 N ARG B 2 SHEET 5 AA3 5 LEU B 64 THR B 80 -1 N ASP B 75 O MSE B 91 SHEET 1 AA4 4 GLY B 38 GLY B 39 0 SHEET 2 AA4 4 ARG B 2 ASN B 13 -1 N VAL B 7 O GLY B 38 SHEET 3 AA4 4 HIS B 16 MSE B 22 -1 O HIS B 16 N ASN B 13 SHEET 4 AA4 4 PHE B 111 LYS B 118 -1 O ASP B 112 N LYS B 21 LINK C ALA A 0 N AMSE A 1 1555 1555 1.33 LINK C ALA A 0 N BMSE A 1 1555 1555 1.34 LINK C AMSE A 1 N ARG A 2 1555 1555 1.33 LINK C BMSE A 1 N ARG A 2 1555 1555 1.34 LINK C LYS A 21 N MSE A 22 1555 1555 1.33 LINK C MSE A 22 N ALA A 23 1555 1555 1.34 LINK C TYR A 90 N AMSE A 91 1555 1555 1.34 LINK C TYR A 90 N BMSE A 91 1555 1555 1.33 LINK C AMSE A 91 N ILE A 92 1555 1555 1.33 LINK C BMSE A 91 N ILE A 92 1555 1555 1.33 LINK C ALA B 0 N AMSE B 1 1555 1555 1.33 LINK C ALA B 0 N BMSE B 1 1555 1555 1.33 LINK C AMSE B 1 N AARG B 2 1555 1555 1.34 LINK C BMSE B 1 N BARG B 2 1555 1555 1.33 LINK C ALYS B 21 N AMSE B 22 1555 1555 1.34 LINK C BLYS B 21 N BMSE B 22 1555 1555 1.34 LINK C AMSE B 22 N ALA B 23 1555 1555 1.34 LINK C BMSE B 22 N ALA B 23 1555 1555 1.34 LINK C TYR B 90 N MSE B 91 1555 1555 1.33 LINK C MSE B 91 N ILE B 92 1555 1555 1.33 SITE 1 AC1 12 ARG B 4 ILE B 6 CYS B 8 MSE B 22 SITE 2 AC1 12 GLY B 37 GLY B 38 LYS B 79 ALA B 130 SITE 3 AC1 12 HOH B 301 HOH B 314 HOH B 380 HOH B 395 CRYST1 33.140 39.346 56.294 77.07 80.74 86.20 P 1 2 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 0.030175 -0.002004 -0.004595 0.00000 SCALE2 0.000000 0.025472 -0.005644 0.00000 SCALE3 0.000000 0.000000 0.018435 0.00000