HEADER HYDROLASE 23-DEC-10 3Q46 TITLE MAGNESIUM ACTIVATED INORGANIC PYROPHOSPHATASE FROM THERMOCOCCUS TITLE 2 THIOREDUCENS BOUND TO HYDROLYZED PRODUCT AT 0.99 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TT-IPPASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS THIOREDUCENS; SOURCE 3 ORGANISM_TAXID: 277988; SOURCE 4 STRAIN: OGL-20; SOURCE 5 GENE: TT-IPPASE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS INORGANIC PYROPHOSPHATASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.C.HUGHES,L.COATES,E.J.MEEHAN,J.D.NG REVDAT 4 13-SEP-23 3Q46 1 REMARK LINK REVDAT 3 17-SEP-14 3Q46 1 JRNL REVDAT 2 29-FEB-12 3Q46 1 JRNL REVDAT 1 04-JAN-12 3Q46 0 JRNL AUTH R.C.HUGHES,L.COATES,M.P.BLAKELEY,S.J.TOMANICEK,P.LANGAN, JRNL AUTH 2 A.Y.KOVALEVSKY,J.M.GARCIA-RUIZ,J.D.NG JRNL TITL INORGANIC PYROPHOSPHATASE CRYSTALS FROM THERMOCOCCUS JRNL TITL 2 THIOREDUCENS FOR X-RAY AND NEUTRON DIFFRACTION. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 68 1482 2012 JRNL REFN ESSN 1744-3091 JRNL PMID 23192028 JRNL DOI 10.1107/S1744309112032447 REMARK 2 REMARK 2 RESOLUTION. 0.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 94537 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.111 REMARK 3 R VALUE (WORKING SET) : 0.110 REMARK 3 FREE R VALUE : 0.123 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 4774 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 18.7604 - 3.0718 0.93 3182 157 0.1534 0.1466 REMARK 3 2 3.0718 - 2.4399 1.00 3310 177 0.1175 0.1424 REMARK 3 3 2.4399 - 2.1320 1.00 3300 165 0.1001 0.0946 REMARK 3 4 2.1320 - 1.9373 1.00 3274 183 0.0926 0.1075 REMARK 3 5 1.9373 - 1.7985 1.00 3274 188 0.0937 0.1022 REMARK 3 6 1.7985 - 1.6926 1.00 3257 177 0.0937 0.1134 REMARK 3 7 1.6926 - 1.6078 0.99 3239 179 0.0874 0.1031 REMARK 3 8 1.6078 - 1.5379 0.99 3233 184 0.0860 0.1097 REMARK 3 9 1.5379 - 1.4787 0.99 3261 157 0.0835 0.1039 REMARK 3 10 1.4787 - 1.4277 0.99 3218 190 0.0829 0.1080 REMARK 3 11 1.4277 - 1.3831 0.99 3236 158 0.0869 0.1115 REMARK 3 12 1.3831 - 1.3435 0.99 3213 167 0.0842 0.0993 REMARK 3 13 1.3435 - 1.3082 0.98 3218 167 0.0871 0.1109 REMARK 3 14 1.3082 - 1.2763 0.98 3183 181 0.0802 0.0942 REMARK 3 15 1.2763 - 1.2473 0.98 3129 182 0.0826 0.1019 REMARK 3 16 1.2473 - 1.2207 0.97 3176 169 0.0852 0.1196 REMARK 3 17 1.2207 - 1.1963 0.97 3169 165 0.0861 0.0995 REMARK 3 18 1.1963 - 1.1737 0.98 3194 150 0.0849 0.1042 REMARK 3 19 1.1737 - 1.1528 0.97 3162 155 0.0866 0.1064 REMARK 3 20 1.1528 - 1.1332 0.97 3139 157 0.0851 0.0982 REMARK 3 21 1.1332 - 1.1150 0.96 3127 172 0.0968 0.1052 REMARK 3 22 1.1150 - 1.0978 0.95 3104 165 0.1135 0.1318 REMARK 3 23 1.0978 - 1.0817 0.93 3002 165 0.1305 0.1588 REMARK 3 24 1.0817 - 1.0664 0.93 2989 163 0.1537 0.1551 REMARK 3 25 1.0664 - 1.0520 0.89 2911 146 0.1725 0.2139 REMARK 3 26 1.0520 - 1.0384 0.86 2796 138 0.1943 0.1964 REMARK 3 27 1.0384 - 1.0254 0.79 2556 133 0.2215 0.2215 REMARK 3 28 1.0254 - 1.0130 0.68 2169 133 0.2447 0.2443 REMARK 3 29 1.0130 - 1.0013 0.51 1618 102 0.2856 0.2769 REMARK 3 30 1.0013 - 0.9900 0.34 1124 49 0.3399 0.3857 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.00 REMARK 3 SHRINKAGE RADIUS : 0.00 REMARK 3 K_SOL : 0.58 REMARK 3 B_SOL : 131.9 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 6.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.03490 REMARK 3 B22 (A**2) : 1.03490 REMARK 3 B33 (A**2) : -2.25060 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.026 1810 REMARK 3 ANGLE : 2.152 2474 REMARK 3 CHIRALITY : 0.124 245 REMARK 3 PLANARITY : 0.015 328 REMARK 3 DIHEDRAL : 15.651 728 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3Q46 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063171. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-08 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 : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : GRAPHITE 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 : 94537 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.950 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 (%) : 82.0 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 4.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.00 REMARK 200 R MERGE FOR SHELL (I) : 0.67400 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: MOLREP REMARK 200 STARTING MODEL: 1UDE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, ISOPROPANOL, MAGNESIUM REMARK 280 CHLORIDE, SODIUM PYROPHOSPHATE, PH 7.5, COUNTER DIFFUSION, FREE- REMARK 280 INTERFACE DIFFUSION, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 49.62650 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 28.65187 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 32.85233 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 49.62650 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 28.65187 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 32.85233 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 49.62650 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 28.65187 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 32.85233 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 49.62650 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 28.65187 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 32.85233 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 49.62650 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 28.65187 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 32.85233 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 49.62650 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 28.65187 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 32.85233 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 57.30375 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 65.70467 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 57.30375 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 65.70467 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 57.30375 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 65.70467 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 57.30375 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 65.70467 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 57.30375 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 65.70467 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 57.30375 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 65.70467 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 23850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -405.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 99.25300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 49.62650 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 85.95562 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 49.62650 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 -28.65187 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 -32.85233 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 0.000000 57.30375 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 -32.85233 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 99.25300 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 57.30375 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 -32.85233 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 224 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 238 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 243 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 288 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 320 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 380 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 396 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 414 LIES ON A SPECIAL POSITION. 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 GLU A 6 CG CD OE1 OE2 REMARK 470 PHE A 174 O 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 NE2 GLN A 138 O HOH A 400 1.73 REMARK 500 CD GLN A 138 O HOH A 400 1.97 REMARK 500 OE1 GLN A 61 O HOH A 404 2.05 REMARK 500 CB ARG A 44 O HOH A 409 2.11 REMARK 500 OD2 ASP A 34 O HOH A 375 2.18 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 418 O HOH A 419 5555 1.07 REMARK 500 O HOH A 366 O HOH A 382 5555 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 12 CB GLU A 12 CG -0.115 REMARK 500 TYR A 47 CE2 TYR A 47 CD2 0.095 REMARK 500 GLU A 87 CD GLU A 87 OE1 0.134 REMARK 500 GLU A 97 CB GLU A 97 CG -0.124 REMARK 500 GLU A 142 CB GLU A 142 CG -0.140 REMARK 500 GLU A 142 CD GLU A 142 OE1 0.069 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 44 NE - CZ - NH2 ANGL. DEV. = -6.4 DEGREES REMARK 500 GLU A 87 OE1 - CD - OE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 GLU A 157 OE1 - CD - OE2 ANGL. DEV. = -7.2 DEGREES 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 ASN A 2 116.68 -15.31 REMARK 500 ASP A 103 41.27 -156.62 REMARK 500 GLU A 177 -111.30 -62.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 44 VAL A 45 135.26 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 ASP A 43 -10.06 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 308 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 32 OE1 REMARK 620 2 HOH A 232 O 88.2 REMARK 620 3 PO4 A 301 O3 92.2 175.3 REMARK 620 4 HOH A 455 O 88.3 90.7 94.0 REMARK 620 5 HOH A 457 O 176.3 88.1 91.5 91.3 REMARK 620 6 HOH A 458 O 91.5 88.6 86.7 179.2 88.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 306 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 66 OD2 REMARK 620 2 ASP A 71 OD1 169.2 REMARK 620 3 ASP A 103 OD1 84.5 85.7 REMARK 620 4 PO4 A 301 O2 96.2 89.6 97.1 REMARK 620 5 PO4 A 301 O4 92.5 98.2 164.2 67.7 REMARK 620 6 HOH A 454 O 87.6 89.3 98.6 164.0 96.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 305 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 71 OD2 REMARK 620 2 HOH A 184 O 91.7 REMARK 620 3 HOH A 185 O 168.1 85.7 REMARK 620 4 PO4 A 301 O4 97.2 92.1 94.5 REMARK 620 5 PO4 A 301 O1 97.1 159.2 89.3 68.1 REMARK 620 6 HOH A 465 O 83.4 98.3 85.5 169.5 101.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 307 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 98 OD2 REMARK 620 2 ASP A 103 OD2 94.7 REMARK 620 3 HOH A 211 O 89.7 88.8 REMARK 620 4 HOH A 213 O 92.6 92.7 177.1 REMARK 620 5 HOH A 218 O 85.6 179.6 91.1 87.3 REMARK 620 6 PO4 A 301 O2 174.4 89.9 87.5 90.1 89.7 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 PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPE A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 310 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3I98 RELATED DB: PDB REMARK 900 X-RAY CRYSTALLOGRAPHIC STRUCTURE OF INORGANIC PYROPHOSPHATASE AT REMARK 900 298K FROM ARCHAEON THERMOCOCCUS THIOREDUCENS REMARK 900 RELATED ID: 3Q3L RELATED DB: PDB REMARK 900 RELATED ID: 3Q4W RELATED DB: PDB REMARK 900 RELATED ID: 3Q5V RELATED DB: PDB DBREF 3Q46 A 1 178 PDB 3Q46 3Q46 1 178 SEQRES 1 A 178 MET ASN PRO PHE HIS GLU LEU GLU PRO GLY PRO GLU VAL SEQRES 2 A 178 PRO GLU VAL VAL TYR ALA LEU ILE GLU ILE PRO LYS GLY SEQRES 3 A 178 SER ARG ASN LYS TYR GLU LEU ASP LYS ALA THR GLY LEU SEQRES 4 A 178 LEU LYS LEU ASP ARG VAL LEU TYR SER PRO PHE PHE TYR SEQRES 5 A 178 PRO VAL ASP TYR GLY ILE ILE PRO GLN THR TRP TYR ASP SEQRES 6 A 178 ASP GLY ASP PRO PHE ASP ILE MET VAL ILE MET ARG GLU SEQRES 7 A 178 PRO VAL TYR PRO LEU THR ILE ILE GLU ALA ARG PRO ILE SEQRES 8 A 178 GLY ILE MET LYS MET GLU ASP SER GLY ASP LYS ASP TRP SEQRES 9 A 178 LYS VAL LEU ALA VAL PRO VAL GLU ASP PRO TYR PHE ASN SEQRES 10 A 178 ASP TRP LYS ASP ILE SER ASP VAL PRO LYS ALA PHE LEU SEQRES 11 A 178 ASP GLU ILE ALA HIS PHE PHE GLN ARG TYR LYS GLU LEU SEQRES 12 A 178 GLN GLY LYS THR THR LYS ILE GLU GLY TRP GLY ASN ALA SEQRES 13 A 178 GLU GLU ALA LYS ARG GLU ILE LEU ARG ALA ILE GLU MET SEQRES 14 A 178 TYR LYS GLU LYS PHE GLY LYS GLU GLU HET PO4 A 301 5 HET MG A 305 1 HET MG A 306 1 HET MG A 307 1 HET MG A 308 1 HET EPE A 309 15 HET CL A 310 1 HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM CL CHLORIDE ION HETSYN EPE HEPES FORMUL 2 PO4 O4 P 3- FORMUL 3 MG 4(MG 2+) FORMUL 7 EPE C8 H18 N2 O4 S FORMUL 8 CL CL 1- FORMUL 9 HOH *295(H2 O) HELIX 1 1 ASP A 113 ASN A 117 5 5 HELIX 2 2 ASP A 121 VAL A 125 5 5 HELIX 3 3 PRO A 126 TYR A 140 1 15 HELIX 4 4 LYS A 141 GLY A 145 5 5 HELIX 5 5 ALA A 156 GLU A 177 1 22 SHEET 1 A 8 ASP A 101 LYS A 102 0 SHEET 2 A 8 THR A 148 ASN A 155 0 SHEET 3 A 8 VAL A 17 ILE A 23 0 SHEET 4 A 8 ASP A 55 ILE A 58 -1 O ILE A 58 N LEU A 20 SHEET 5 A 8 ASP A 71 VAL A 74 -1 O VAL A 74 N ASP A 55 SHEET 6 A 8 LYS A 105 PRO A 110 1 O VAL A 106 N MET A 73 SHEET 7 A 8 ILE A 85 ASP A 98 -1 N ILE A 91 O LEU A 107 SHEET 8 A 8 THR A 148 ASN A 155 -1 O GLY A 154 N ILE A 93 SHEET 1 B 2 ASN A 29 LEU A 33 0 SHEET 2 B 2 LEU A 40 VAL A 45 -1 O ARG A 44 N LYS A 30 LINK OE1 GLU A 32 MG MG A 308 1555 1555 2.08 LINK OD2 ASP A 66 MG MG A 306 1555 1555 2.09 LINK OD2 ASP A 71 MG MG A 305 1555 1555 2.02 LINK OD1 ASP A 71 MG MG A 306 1555 1555 2.09 LINK OD2 ASP A 98 MG MG A 307 1555 1555 2.02 LINK OD1 ASP A 103 MG MG A 306 1555 1555 2.08 LINK OD2 ASP A 103 MG MG A 307 1555 1555 2.03 LINK O HOH A 184 MG MG A 305 1555 1555 2.06 LINK O HOH A 185 MG MG A 305 1555 1555 2.09 LINK O HOH A 211 MG MG A 307 1555 1555 2.11 LINK O HOH A 213 MG MG A 307 1555 1555 2.11 LINK O HOH A 218 MG MG A 307 1555 1555 2.10 LINK O HOH A 232 MG MG A 308 1555 1555 2.06 LINK O4 PO4 A 301 MG MG A 305 1555 1555 2.12 LINK O1 PO4 A 301 MG MG A 305 1555 1555 2.19 LINK O2 PO4 A 301 MG MG A 306 1555 1555 2.17 LINK O4 PO4 A 301 MG MG A 306 1555 1555 2.18 LINK O2 PO4 A 301 MG MG A 307 1555 1555 2.05 LINK O3 PO4 A 301 MG MG A 308 1555 1555 2.02 LINK MG MG A 305 O HOH A 465 1555 1555 2.04 LINK MG MG A 306 O HOH A 454 1555 1555 2.05 LINK MG MG A 308 O HOH A 455 1555 1555 2.05 LINK MG MG A 308 O HOH A 457 1555 1555 2.10 LINK MG MG A 308 O HOH A 458 1555 1555 2.06 CISPEP 1 VAL A 13 PRO A 14 0 -1.40 SITE 1 AC1 19 LYS A 30 GLU A 32 TYR A 56 ASP A 66 SITE 2 AC1 19 ASP A 71 ASP A 103 LYS A 105 HOH A 184 SITE 3 AC1 19 HOH A 185 HOH A 211 HOH A 213 HOH A 218 SITE 4 AC1 19 MG A 305 MG A 306 MG A 307 MG A 308 SITE 5 AC1 19 HOH A 455 HOH A 457 HOH A 458 SITE 1 AC2 6 ASP A 71 HOH A 184 HOH A 185 PO4 A 301 SITE 2 AC2 6 MG A 306 HOH A 465 SITE 1 AC3 7 ASP A 66 ASP A 71 ASP A 103 PO4 A 301 SITE 2 AC3 7 MG A 305 MG A 307 HOH A 454 SITE 1 AC4 7 ASP A 98 ASP A 103 HOH A 211 HOH A 213 SITE 2 AC4 7 HOH A 218 PO4 A 301 MG A 306 SITE 1 AC5 6 GLU A 32 HOH A 232 PO4 A 301 HOH A 455 SITE 2 AC5 6 HOH A 457 HOH A 458 SITE 1 AC6 18 ARG A 44 ASP A 65 ASP A 66 GLY A 67 SITE 2 AC6 18 ASP A 98 ASP A 101 LYS A 141 GLY A 145 SITE 3 AC6 18 LYS A 146 THR A 147 HOH A 218 HOH A 236 SITE 4 AC6 18 HOH A 351 HOH A 367 HOH A 373 HOH A 408 SITE 5 AC6 18 HOH A 419 HOH A 455 SITE 1 AC7 6 LYS A 30 TYR A 52 TYR A 56 TYR A 140 SITE 2 AC7 6 HOH A 211 HOH A 386 CRYST1 99.253 99.253 98.557 90.00 90.00 120.00 H 3 2 18 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 0.010075 0.005817 0.000000 0.00000 SCALE2 0.000000 0.011634 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010146 0.00000