HEADER HYDROLASE 08-MAY-07 2Z1J TITLE CRYSTAL STRUCTURE OF E.COLI RNASE HI SURFACE CHARGED TITLE 2 MUTANT(Q4R/T40E/Q72H/Q76K/Q80E/T92K/Q105K/Q113R/Q115K/N143K/T145K) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE HI; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE HI, RIBONUCLEASE H, RNASE H; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: MIC2067(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET25B KEYWDS RNASE HI, THERMOSTABILITY, SURFACE-CHARGE RESIDUE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.J.YOU,S.FUKUCHI,K.NISHIKAWA,Y.KOGA,K.TAKANO,S.KANAYA REVDAT 4 01-NOV-23 2Z1J 1 REMARK REVDAT 3 10-NOV-21 2Z1J 1 SEQADV REVDAT 2 24-FEB-09 2Z1J 1 VERSN REVDAT 1 13-NOV-07 2Z1J 0 JRNL AUTH D.-J.YOU,S.FUKUCHI,K.NISHIKAWA,Y.KOGA,K.TAKANO,S.KANAYA JRNL TITL PROTEIN THERMOSTABILIZATION REQUIRES A FINE-TUNED PLACEMENT JRNL TITL 2 OF SURFACE-CHARGED RESIDUES JRNL REF J.BIOCHEM.(TOKYO) V. 142 507 2007 JRNL REFN ISSN 0021-924X JRNL PMID 17761696 JRNL DOI 10.1093/JB/MVM157 REMARK 2 REMARK 2 RESOLUTION. 2.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1089803.860 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 8828 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 SET) : 0.208 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 468 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.53 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1343 REMARK 3 BIN R VALUE (WORKING SET) : 0.2340 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 76 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1217 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.00000 REMARK 3 B22 (A**2) : 2.00000 REMARK 3 B33 (A**2) : -4.00000 REMARK 3 B12 (A**2) : 5.58000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.22 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.130 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.060 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.700 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.960 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.020 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 38.37 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2Z1J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000027403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-05 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 : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9722 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2RN2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM HEPES-NAOH, 15-25% PEG 3350, PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.01600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 17.00800 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 17.00800 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 34.01600 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: MONOMERIC 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 GLN A 152 REMARK 465 VAL A 153 REMARK 465 GLU A 154 REMARK 465 VAL A 155 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 GLU A 80 -67.91 -128.11 REMARK 500 LYS A 95 6.99 81.79 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 TRP A 81 -14.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z1G RELATED DB: PDB REMARK 900 THE MUTANT(Q4R/T40E/Q72H/Q76K/Q80E/T92K/Q105K) OF THE SAME PROTEIN REMARK 900 RELATED ID: 2Z1H RELATED DB: PDB REMARK 900 THE MUTANT(Q4R/T92K/Q105K/Q113R/Q115K/N143K/T145K) OF THE SAME REMARK 900 PROTEIN REMARK 900 RELATED ID: 2Z1I RELATED DB: PDB REMARK 900 THE MUTANT(Q4R/T40E/Q72H/Q76K/Q80E/T92K/Q105K/Q113R/Q115K) OF THE REMARK 900 SAME PROTEIN DBREF 2Z1J A 1 155 UNP P0A7Y4 RNH_ECOLI 1 155 SEQADV 2Z1J ARG A 4 UNP P0A7Y4 GLN 4 ENGINEERED MUTATION SEQADV 2Z1J GLU A 40 UNP P0A7Y4 THR 40 ENGINEERED MUTATION SEQADV 2Z1J HIS A 72 UNP P0A7Y4 GLN 72 ENGINEERED MUTATION SEQADV 2Z1J LYS A 76 UNP P0A7Y4 GLN 76 ENGINEERED MUTATION SEQADV 2Z1J GLU A 80 UNP P0A7Y4 GLN 80 ENGINEERED MUTATION SEQADV 2Z1J LYS A 92 UNP P0A7Y4 THR 92 ENGINEERED MUTATION SEQADV 2Z1J LYS A 105 UNP P0A7Y4 GLN 105 ENGINEERED MUTATION SEQADV 2Z1J ARG A 113 UNP P0A7Y4 GLN 113 ENGINEERED MUTATION SEQADV 2Z1J LYS A 115 UNP P0A7Y4 GLN 115 ENGINEERED MUTATION SEQADV 2Z1J LYS A 143 UNP P0A7Y4 ASN 143 ENGINEERED MUTATION SEQADV 2Z1J LYS A 145 UNP P0A7Y4 THR 145 ENGINEERED MUTATION SEQRES 1 A 155 MET LEU LYS ARG VAL GLU ILE PHE THR ASP GLY SER CYS SEQRES 2 A 155 LEU GLY ASN PRO GLY PRO GLY GLY TYR GLY ALA ILE LEU SEQRES 3 A 155 ARG TYR ARG GLY ARG GLU LYS THR PHE SER ALA GLY TYR SEQRES 4 A 155 GLU ARG THR THR ASN ASN ARG MET GLU LEU MET ALA ALA SEQRES 5 A 155 ILE VAL ALA LEU GLU ALA LEU LYS GLU HIS CYS GLU VAL SEQRES 6 A 155 ILE LEU SER THR ASP SER HIS TYR VAL ARG LYS GLY ILE SEQRES 7 A 155 THR GLU TRP ILE HIS ASN TRP LYS LYS ARG GLY TRP LYS SEQRES 8 A 155 LYS ALA ASP LYS LYS PRO VAL LYS ASN VAL ASP LEU TRP SEQRES 9 A 155 LYS ARG LEU ASP ALA ALA LEU GLY ARG HIS LYS ILE LYS SEQRES 10 A 155 TRP GLU TRP VAL LYS GLY HIS ALA GLY HIS PRO GLU ASN SEQRES 11 A 155 GLU ARG CYS ASP GLU LEU ALA ARG ALA ALA ALA MET LYS SEQRES 12 A 155 PRO LYS LEU GLU ASP THR GLY TYR GLN VAL GLU VAL FORMUL 2 HOH *43(H2 O) HELIX 1 1 THR A 43 LEU A 59 1 17 HELIX 2 2 SER A 71 GLU A 80 1 10 HELIX 3 3 GLU A 80 LYS A 87 1 8 HELIX 4 4 ASN A 100 GLY A 112 1 13 HELIX 5 5 HIS A 127 LYS A 143 1 17 SHEET 1 A 5 ARG A 31 THR A 42 0 SHEET 2 A 5 GLY A 18 TYR A 28 -1 N GLY A 20 O TYR A 39 SHEET 3 A 5 LYS A 3 CYS A 13 -1 N ASP A 10 O GLY A 23 SHEET 4 A 5 CYS A 63 THR A 69 1 O GLU A 64 N LYS A 3 SHEET 5 A 5 LYS A 115 TRP A 120 1 O GLU A 119 N LEU A 67 CISPEP 1 ASN A 16 PRO A 17 0 -0.71 CRYST1 85.273 85.273 51.024 90.00 90.00 120.00 P 32 2 1 6 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 0.011727 0.006771 0.000000 0.00000 SCALE2 0.000000 0.013541 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019599 0.00000