HEADER HYDROLASE 19-MAY-14 4QF4 TITLE CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT V23M AT CRYOGENIC TITLE 2 TEMPERATURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THERMONUCLEASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TNASE, MICROCOCCAL NUCLEASE, STAPHYLOCOCCAL NUCLEASE, COMPND 5 NUCLEASE B, NUCLEASE A; COMPND 6 EC: 3.1.31.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: NUC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET24A+ KEYWDS STAPHYLOCOCCAL NUCLEASE, HYDROLASE, PDTP, CAVITY, PRESSURE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.CARO,J.L.SCHLESSMAN,A.HEROUX,E.B.GARCIA-MORENO REVDAT 3 20-SEP-23 4QF4 1 REMARK SEQADV LINK REVDAT 2 22-NOV-17 4QF4 1 REMARK REVDAT 1 04-JUN-14 4QF4 0 JRNL AUTH J.A.CARO,J.L.SCHLESSMAN,E.B.GARCIA-MORENO JRNL TITL PRESSURE EFFECTS IN PROTEINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 26206 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) : 0.208 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1329 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1781 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2122 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.09000 REMARK 3 B22 (A**2) : 1.09000 REMARK 3 B33 (A**2) : -2.18000 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): 0.148 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.135 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.911 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2270 ; 0.018 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3067 ; 1.905 ; 2.009 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 276 ; 6.450 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;34.629 ;24.681 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 449 ;16.743 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;14.306 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 331 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1628 ; 0.011 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 6 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 7 A 32 REMARK 3 ORIGIN FOR THE GROUP (A): 9.3817 4.2852 15.8893 REMARK 3 T TENSOR REMARK 3 T11: 0.0569 T22: 0.2299 REMARK 3 T33: 0.0787 T12: -0.0428 REMARK 3 T13: -0.0061 T23: -0.0171 REMARK 3 L TENSOR REMARK 3 L11: 4.3378 L22: 3.9849 REMARK 3 L33: 5.1247 L12: 0.3269 REMARK 3 L13: -1.5377 L23: -0.5217 REMARK 3 S TENSOR REMARK 3 S11: -0.1502 S12: 0.2526 S13: -0.3989 REMARK 3 S21: 0.2240 S22: 0.3820 S23: -0.0135 REMARK 3 S31: 0.2978 S32: -0.6098 S33: -0.2318 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 33 A 96 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7405 13.0571 13.2154 REMARK 3 T TENSOR REMARK 3 T11: 0.0943 T22: 0.2519 REMARK 3 T33: 0.0710 T12: 0.0251 REMARK 3 T13: 0.0111 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 2.2295 L22: 2.1247 REMARK 3 L33: 4.8136 L12: 0.4157 REMARK 3 L13: -1.4697 L23: -2.3487 REMARK 3 S TENSOR REMARK 3 S11: -0.0423 S12: 0.1992 S13: 0.0540 REMARK 3 S21: 0.1088 S22: 0.3944 S23: 0.1157 REMARK 3 S31: -0.3218 S32: -0.7033 S33: -0.3521 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 97 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6178 22.1692 9.5111 REMARK 3 T TENSOR REMARK 3 T11: 0.2433 T22: 0.1082 REMARK 3 T33: 0.0597 T12: -0.0257 REMARK 3 T13: 0.0360 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 1.5531 L22: 4.3080 REMARK 3 L33: 7.7501 L12: 0.2638 REMARK 3 L13: -1.1669 L23: -3.2761 REMARK 3 S TENSOR REMARK 3 S11: 0.1431 S12: 0.1650 S13: 0.1076 REMARK 3 S21: 0.5085 S22: 0.0486 S23: -0.2558 REMARK 3 S31: -1.2922 S32: 0.0209 S33: -0.1917 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 7 B 30 REMARK 3 ORIGIN FOR THE GROUP (A): 24.0374 29.1366 -16.0620 REMARK 3 T TENSOR REMARK 3 T11: 0.0568 T22: 0.1817 REMARK 3 T33: 0.0755 T12: -0.0473 REMARK 3 T13: 0.0055 T23: 0.0314 REMARK 3 L TENSOR REMARK 3 L11: 4.1503 L22: 4.0721 REMARK 3 L33: 4.4064 L12: 0.0040 REMARK 3 L13: 0.7995 L23: 1.0337 REMARK 3 S TENSOR REMARK 3 S11: -0.1608 S12: 0.2865 S13: 0.3640 REMARK 3 S21: 0.1777 S22: 0.3887 S23: -0.0071 REMARK 3 S31: -0.2338 S32: 0.5002 S33: -0.2279 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 31 B 96 REMARK 3 ORIGIN FOR THE GROUP (A): 24.3140 20.8800 -18.1192 REMARK 3 T TENSOR REMARK 3 T11: 0.0745 T22: 0.2374 REMARK 3 T33: 0.0800 T12: -0.0051 REMARK 3 T13: -0.0144 T23: 0.0133 REMARK 3 L TENSOR REMARK 3 L11: 2.2445 L22: 2.2045 REMARK 3 L33: 4.3664 L12: 0.2854 REMARK 3 L13: 1.2962 L23: 2.0284 REMARK 3 S TENSOR REMARK 3 S11: -0.0416 S12: 0.2341 S13: -0.0359 REMARK 3 S21: 0.0274 S22: 0.3769 S23: -0.1269 REMARK 3 S31: 0.2031 S32: 0.5879 S33: -0.3353 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 97 B 141 REMARK 3 ORIGIN FOR THE GROUP (A): 16.4373 11.3048 -21.9061 REMARK 3 T TENSOR REMARK 3 T11: 0.2576 T22: 0.1435 REMARK 3 T33: 0.0981 T12: -0.0474 REMARK 3 T13: -0.0605 T23: 0.0274 REMARK 3 L TENSOR REMARK 3 L11: 1.6746 L22: 4.4095 REMARK 3 L33: 7.3748 L12: 0.4619 REMARK 3 L13: 1.7469 L23: 4.1027 REMARK 3 S TENSOR REMARK 3 S11: 0.1776 S12: 0.2084 S13: -0.1454 REMARK 3 S21: 0.4633 S22: 0.0477 S23: 0.2729 REMARK 3 S31: 1.2102 S32: -0.0416 S33: -0.2254 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 4QF4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAY-14. REMARK 100 THE DEPOSITION ID IS D_1000085975. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-SEP-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : MONOCHROMATOR: DOUBLE REMARK 200 SILICON(111) CRYSTAL REMARK 200 MONOCHROMATOR WITH CRYOGENICALLY- REMARK 200 COOLED FIRST CRYSTAL AND REMARK 200 SAGITTALLY- BENT SECOND CRYSTAL REMARK 200 HORIZONTALLY- FOCUSING AT 3.3:1 REMARK 200 DEMAGNIFICATION. MIRROR: REMARK 200 MERIDIONALLY- BENT FUSED SILICA REMARK 200 MIRROR WITH PALLADIUM AND REMARK 200 UNCOATED STRIPES VERTICALLY- REMARK 200 FOCUSING AT 6.6:1 DEMAGNIFICATION REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26669 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.70 REMARK 200 R MERGE FOR SHELL (I) : 0.31600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 9.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: PDB ENTRY 1SNC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32% MPD, 25 MM POTASSIUM PHOSPHATE, REMARK 280 CALCIUM CHLORIDE, PDTP, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 31.40850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 15.70425 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.11275 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 ALA A 1 REMARK 465 THR A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 LYS A 5 REMARK 465 LYS A 6 REMARK 465 GLY A 48 REMARK 465 LYS A 49 REMARK 465 LYS A 50 REMARK 465 GLU A 142 REMARK 465 ASP A 143 REMARK 465 ASN A 144 REMARK 465 ALA A 145 REMARK 465 ASP A 146 REMARK 465 SER A 147 REMARK 465 GLY A 148 REMARK 465 GLN A 149 REMARK 465 ALA B 1 REMARK 465 THR B 2 REMARK 465 SER B 3 REMARK 465 THR B 4 REMARK 465 LYS B 5 REMARK 465 LYS B 6 REMARK 465 GLY B 48 REMARK 465 LYS B 49 REMARK 465 LYS B 50 REMARK 465 GLU B 142 REMARK 465 ASP B 143 REMARK 465 ASN B 144 REMARK 465 ALA B 145 REMARK 465 ASP B 146 REMARK 465 SER B 147 REMARK 465 GLY B 148 REMARK 465 GLN B 149 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 ASP A 19 -156.11 -149.29 REMARK 500 TYR A 54 -3.70 90.20 REMARK 500 ASN A 119 24.82 -144.50 REMARK 500 ASN A 138 -105.06 47.10 REMARK 500 ILE B 18 -60.01 -99.15 REMARK 500 ASP B 19 -151.29 -144.21 REMARK 500 TYR B 54 0.06 88.62 REMARK 500 ASN B 119 22.40 -141.96 REMARK 500 ASN B 138 -102.89 43.98 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 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD1 REMARK 620 2 ASP A 40 OD1 94.6 REMARK 620 3 THR A 41 O 92.6 76.8 REMARK 620 4 THP A 201 O4P 96.5 73.1 149.1 REMARK 620 5 HOH A 320 O 81.8 144.4 68.1 142.4 REMARK 620 6 HOH A 330 O 77.0 142.3 139.4 71.5 71.6 REMARK 620 7 HOH A 331 O 175.2 85.0 82.7 88.0 95.8 106.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 21 OD1 REMARK 620 2 ASP B 40 OD1 89.2 REMARK 620 3 THR B 41 O 94.4 81.0 REMARK 620 4 THP B 201 O4P 94.5 70.5 150.0 REMARK 620 5 HOH B 311 O 76.0 139.7 136.5 73.5 REMARK 620 6 HOH B 322 O 80.4 145.7 67.4 142.4 69.2 REMARK 620 7 HOH B 325 O 176.6 93.8 84.7 87.9 102.4 96.3 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THP B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1SNC RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF STAPHYLOCOCCAL REMARK 900 NUCLEASE, CA2+, AND THE INHIBITOR PD*TP, REFINED AT 1.65 ANGSTROMS REMARK 900 RELATED ID: 4K5W RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT V23M/L25F/T62F REMARK 900 AT CRYOGENIC TEMPERATURE REMARK 900 RELATED ID: 4K5X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT V23M/L36F AT REMARK 900 CRYOGENIC TEMPERATURE REMARK 900 RELATED ID: 4K6D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT V23M/T62F AT REMARK 900 CRYOGENIC TEMPERATURE REMARK 900 RELATED ID: 3PMF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STAPHYLOCOCCAL NUCLEASE VARIANT DELTA+PHS V23A REMARK 900 AT CRYOGENIC TEMPERATURE DBREF 4QF4 A 1 149 UNP P00644 NUC_STAAU 83 231 DBREF 4QF4 B 1 149 UNP P00644 NUC_STAAU 83 231 SEQADV 4QF4 MET A 23 UNP P00644 VAL 105 ENGINEERED MUTATION SEQADV 4QF4 GLY A 48 UNP P00644 LYS 130 CONFLICT SEQADV 4QF4 LYS A 50 UNP P00644 GLY 132 CONFLICT SEQADV 4QF4 MET B 23 UNP P00644 VAL 105 ENGINEERED MUTATION SEQADV 4QF4 GLY B 48 UNP P00644 LYS 130 CONFLICT SEQADV 4QF4 LYS B 50 UNP P00644 GLY 132 CONFLICT SEQRES 1 A 149 ALA THR SER THR LYS LYS LEU HIS LYS GLU PRO ALA THR SEQRES 2 A 149 LEU ILE LYS ALA ILE ASP GLY ASP THR MET LYS LEU MET SEQRES 3 A 149 TYR LYS GLY GLN PRO MET THR PHE ARG LEU LEU LEU VAL SEQRES 4 A 149 ASP THR PRO GLU THR LYS HIS PRO GLY LYS LYS VAL GLU SEQRES 5 A 149 LYS TYR GLY PRO GLU ALA SER ALA PHE THR LYS LYS MET SEQRES 6 A 149 VAL GLU ASN ALA LYS LYS ILE GLU VAL GLU PHE ASP LYS SEQRES 7 A 149 GLY GLN ARG THR ASP LYS TYR GLY ARG GLY LEU ALA TYR SEQRES 8 A 149 ILE TYR ALA ASP GLY LYS MET VAL ASN GLU ALA LEU VAL SEQRES 9 A 149 ARG GLN GLY LEU ALA LYS VAL ALA TYR VAL TYR LYS PRO SEQRES 10 A 149 ASN ASN THR HIS GLU GLN HIS LEU ARG LYS SER GLU ALA SEQRES 11 A 149 GLN ALA LYS LYS GLU LYS LEU ASN ILE TRP SER GLU ASP SEQRES 12 A 149 ASN ALA ASP SER GLY GLN SEQRES 1 B 149 ALA THR SER THR LYS LYS LEU HIS LYS GLU PRO ALA THR SEQRES 2 B 149 LEU ILE LYS ALA ILE ASP GLY ASP THR MET LYS LEU MET SEQRES 3 B 149 TYR LYS GLY GLN PRO MET THR PHE ARG LEU LEU LEU VAL SEQRES 4 B 149 ASP THR PRO GLU THR LYS HIS PRO GLY LYS LYS VAL GLU SEQRES 5 B 149 LYS TYR GLY PRO GLU ALA SER ALA PHE THR LYS LYS MET SEQRES 6 B 149 VAL GLU ASN ALA LYS LYS ILE GLU VAL GLU PHE ASP LYS SEQRES 7 B 149 GLY GLN ARG THR ASP LYS TYR GLY ARG GLY LEU ALA TYR SEQRES 8 B 149 ILE TYR ALA ASP GLY LYS MET VAL ASN GLU ALA LEU VAL SEQRES 9 B 149 ARG GLN GLY LEU ALA LYS VAL ALA TYR VAL TYR LYS PRO SEQRES 10 B 149 ASN ASN THR HIS GLU GLN HIS LEU ARG LYS SER GLU ALA SEQRES 11 B 149 GLN ALA LYS LYS GLU LYS LEU ASN ILE TRP SER GLU ASP SEQRES 12 B 149 ASN ALA ASP SER GLY GLN HET THP A 201 25 HET CA A 202 1 HET PO4 A 203 5 HET THP B 201 25 HET CA B 202 1 HET PO4 B 203 5 HETNAM THP THYMIDINE-3',5'-DIPHOSPHATE HETNAM CA CALCIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 3 THP 2(C10 H16 N2 O11 P2) FORMUL 4 CA 2(CA 2+) FORMUL 5 PO4 2(O4 P 3-) FORMUL 9 HOH *113(H2 O) HELIX 1 1 TYR A 54 ASN A 68 1 15 HELIX 2 2 VAL A 99 GLN A 106 1 8 HELIX 3 3 HIS A 121 GLU A 135 1 15 HELIX 4 4 LEU A 137 SER A 141 5 5 HELIX 5 5 TYR B 54 ASN B 68 1 15 HELIX 6 6 VAL B 99 GLN B 106 1 8 HELIX 7 7 HIS B 121 GLU B 135 1 15 HELIX 8 8 LEU B 137 SER B 141 5 5 SHEET 1 A 7 LYS A 97 MET A 98 0 SHEET 2 A 7 GLY A 88 ALA A 94 -1 N ALA A 94 O LYS A 97 SHEET 3 A 7 ILE A 72 GLU A 75 -1 N GLU A 73 O TYR A 93 SHEET 4 A 7 GLU A 10 ALA A 17 -1 N GLU A 10 O VAL A 74 SHEET 5 A 7 THR A 22 TYR A 27 -1 O MET A 26 N THR A 13 SHEET 6 A 7 GLN A 30 LEU A 36 -1 O PHE A 34 N MET A 23 SHEET 7 A 7 GLY A 88 ALA A 94 1 O GLY A 88 N ARG A 35 SHEET 1 B 2 VAL A 39 ASP A 40 0 SHEET 2 B 2 LYS A 110 VAL A 111 -1 O LYS A 110 N ASP A 40 SHEET 1 C 7 LYS B 97 MET B 98 0 SHEET 2 C 7 GLY B 88 ALA B 94 -1 N ALA B 94 O LYS B 97 SHEET 3 C 7 ILE B 72 GLU B 75 -1 N GLU B 75 O TYR B 91 SHEET 4 C 7 GLU B 10 ALA B 17 -1 N GLU B 10 O VAL B 74 SHEET 5 C 7 THR B 22 TYR B 27 -1 O LYS B 24 N LYS B 16 SHEET 6 C 7 GLN B 30 LEU B 36 -1 O PHE B 34 N MET B 23 SHEET 7 C 7 GLY B 88 ALA B 94 1 O GLY B 88 N ARG B 35 SHEET 1 D 2 VAL B 39 ASP B 40 0 SHEET 2 D 2 LYS B 110 VAL B 111 -1 O LYS B 110 N ASP B 40 LINK OD1 ASP A 21 CA CA A 202 1555 1555 2.50 LINK OD1 ASP A 40 CA CA A 202 1555 1555 2.12 LINK O THR A 41 CA CA A 202 1555 1555 2.57 LINK O4P THP A 201 CA CA A 202 1555 1555 2.81 LINK CA CA A 202 O HOH A 320 1555 1555 2.42 LINK CA CA A 202 O HOH A 330 1555 1555 2.66 LINK CA CA A 202 O HOH A 331 1555 1555 2.34 LINK OD1 ASP B 21 CA CA B 202 1555 1555 2.60 LINK OD1 ASP B 40 CA CA B 202 1555 1555 2.02 LINK O THR B 41 CA CA B 202 1555 1555 2.55 LINK O4P THP B 201 CA CA B 202 1555 1555 2.73 LINK CA CA B 202 O HOH B 311 1555 1555 2.67 LINK CA CA B 202 O HOH B 322 1555 1555 2.46 LINK CA CA B 202 O HOH B 325 1555 1555 2.31 CISPEP 1 LYS A 116 PRO A 117 0 6.38 CISPEP 2 LYS B 116 PRO B 117 0 6.25 SITE 1 AC1 17 ARG A 35 LEU A 36 ASP A 40 LYS A 71 SITE 2 AC1 17 ASP A 83 LYS A 84 TYR A 85 ARG A 87 SITE 3 AC1 17 LEU A 89 TYR A 113 TYR A 115 CA A 202 SITE 4 AC1 17 HOH A 301 HOH A 310 HOH A 330 HOH A 337 SITE 5 AC1 17 HOH A 340 SITE 1 AC2 7 ASP A 21 ASP A 40 THR A 41 THP A 201 SITE 2 AC2 7 HOH A 320 HOH A 330 HOH A 331 SITE 1 AC3 2 MET A 32 THR A 82 SITE 1 AC4 16 ARG B 35 LEU B 36 ASP B 40 LYS B 71 SITE 2 AC4 16 ASP B 83 LYS B 84 TYR B 85 ARG B 87 SITE 3 AC4 16 LEU B 89 TYR B 113 TYR B 115 CA B 202 SITE 4 AC4 16 HOH B 301 HOH B 310 HOH B 311 HOH B 344 SITE 1 AC5 7 ASP B 21 ASP B 40 THR B 41 THP B 201 SITE 2 AC5 7 HOH B 311 HOH B 322 HOH B 325 SITE 1 AC6 1 TYR B 27 CRYST1 67.530 67.530 62.817 90.00 90.00 90.00 P 41 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 0.014808 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014808 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015919 0.00000