HEADER HYDROLASE 19-MAR-11 3R5U TITLE THE STRUCTURE OF MANGANESE BOUND THERMOCOCCUS THIOREDUCENS INORGANIC TITLE 2 PYROPHOSPHATASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TT-IPPASE; COMPND 3 CHAIN: A, B; 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.M.GARCIA-RUIZ,J.D.NG REVDAT 3 13-SEP-23 3R5U 1 REMARK LINK REVDAT 2 24-JAN-18 3R5U 1 AUTHOR JRNL REVDAT 1 28-MAR-12 3R5U 0 JRNL AUTH R.C.HUGHES,L.COATES,E.J.MEEHAN,J.M.GARCIA-RUIZ,J.D.NG JRNL TITL THE STRUCTURE OF MANGANESE BOUND THERMOCOCCUS THIOREDUCENS JRNL TITL 2 INORGANIC PYROPHOSPHATASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.92 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28786 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.196 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1458 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 29.7141 - 4.1305 1.00 2857 128 0.1568 0.1695 REMARK 3 2 4.1305 - 3.2798 1.00 2771 156 0.1431 0.1793 REMARK 3 3 3.2798 - 2.8656 1.00 2747 139 0.1510 0.2099 REMARK 3 4 2.8656 - 2.6038 1.00 2704 167 0.1607 0.1957 REMARK 3 5 2.6038 - 2.4172 1.00 2735 151 0.1483 0.2118 REMARK 3 6 2.4172 - 2.2748 1.00 2710 142 0.1449 0.1983 REMARK 3 7 2.2748 - 2.1609 1.00 2695 149 0.1450 0.2172 REMARK 3 8 2.1609 - 2.0669 1.00 2705 146 0.1434 0.2265 REMARK 3 9 2.0669 - 1.9873 1.00 2735 131 0.1472 0.1950 REMARK 3 10 1.9873 - 1.9200 0.99 2669 149 0.1547 0.2029 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.34 REMARK 3 B_SOL : 41.26 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06440 REMARK 3 B22 (A**2) : 0.06440 REMARK 3 B33 (A**2) : -0.12870 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 : 0.008 3147 REMARK 3 ANGLE : 1.088 4310 REMARK 3 CHIRALITY : 0.080 438 REMARK 3 PLANARITY : 0.005 565 REMARK 3 DIHEDRAL : 13.719 1208 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 3R5U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAR-11. REMARK 100 THE DEPOSITION ID IS D_1000064526. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-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 : 28786 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.99 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.15400 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: 1TWL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES PH 7.5, POLYETHYLENE GLYCOL REMARK 280 8000, ETHYLENE GLYCOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 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 57.25700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 33.05734 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 49.47933 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 57.25700 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 33.05734 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 49.47933 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 57.25700 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 33.05734 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 49.47933 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 57.25700 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 33.05734 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 49.47933 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 57.25700 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 33.05734 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 49.47933 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 57.25700 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 33.05734 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 49.47933 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 66.11469 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 98.95867 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 66.11469 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 98.95867 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 66.11469 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 98.95867 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 66.11469 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 98.95867 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 66.11469 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 98.95867 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 66.11469 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 98.95867 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 300 REMARK: HEXAMER 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: 16800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -133.0 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 -114.51400 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 -57.25700 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -99.17203 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 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 296 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 313 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 407 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 410 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 428 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 295 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 314 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 315 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 372 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 384 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 415 LIES ON A SPECIAL POSITION. 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 LYS A 176 REMARK 465 GLU A 177 REMARK 465 GLU A 178 REMARK 465 LYS B 176 REMARK 465 GLU B 177 REMARK 465 GLU B 178 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 36 CG CD CE NZ REMARK 470 LYS A 120 NZ REMARK 470 LYS A 146 NZ REMARK 470 LYS A 149 CD CE NZ REMARK 470 PHE A 174 O REMARK 470 LYS B 35 CG CD CE NZ REMARK 470 LYS B 36 CG CD CE NZ REMARK 470 LYS B 146 NZ REMARK 470 LYS B 149 CD CE NZ REMARK 470 PHE B 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 O ASP A 34 O THR A 37 1.70 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 ASP A 34 O - C - N ANGL. DEV. = -12.8 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 LYS A 35 10.61 -68.40 REMARK 500 SER B 99 -104.63 -136.26 REMARK 500 ASP B 103 52.64 -111.12 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 34 10.50 REMARK 500 LYS A 35 -10.39 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 MN A 432 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 66 OD2 REMARK 620 2 ASP A 71 OD2 154.0 REMARK 620 3 ASP A 71 OD1 158.8 37.0 REMARK 620 4 ASP A 103 OD1 90.7 84.7 110.4 REMARK 620 5 HOH A 225 O 84.2 107.3 75.2 161.7 REMARK 620 6 HOH A 235 O 77.8 77.5 100.1 97.3 98.8 REMARK 620 7 HOH A 235 O 88.4 68.3 87.4 105.0 92.5 13.1 REMARK 620 8 HOH A 263 O 110.2 94.4 73.1 81.3 84.0 171.8 160.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 433 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 66 OD2 REMARK 620 2 ASP B 71 OD1 165.7 REMARK 620 3 ASP B 103 OD1 83.8 110.6 REMARK 620 4 HOH B 226 O 83.8 93.8 99.6 REMARK 620 5 HOH B 236 O 84.1 82.2 157.7 97.6 REMARK 620 6 HOH B 264 O 101.9 79.3 86.9 171.9 77.4 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 MN A 432 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 433 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3R5V RELATED DB: PDB REMARK 900 RELATED ID: 3R6E RELATED DB: PDB REMARK 900 RELATED ID: 3I98 RELATED DB: PDB REMARK 900 RELATED ID: 3Q3L RELATED DB: PDB REMARK 900 RELATED ID: 3Q46 RELATED DB: PDB REMARK 900 RELATED ID: 3Q4W RELATED DB: PDB REMARK 900 RELATED ID: 3Q5V RELATED DB: PDB REMARK 900 RELATED ID: 3Q9M RELATED DB: PDB DBREF 3R5U A 1 178 PDB 3R5U 3R5U 1 178 DBREF 3R5U B 1 178 PDB 3R5U 3R5U 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 LYS 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 SEQRES 1 B 178 MET ASN PRO PHE HIS GLU LEU GLU PRO GLY PRO GLU VAL SEQRES 2 B 178 PRO GLU VAL VAL TYR ALA LEU ILE GLU ILE PRO LYS GLY SEQRES 3 B 178 SER ARG ASN LYS TYR GLU LEU ASP LYS LYS THR GLY LEU SEQRES 4 B 178 LEU LYS LEU ASP ARG VAL LEU TYR SER PRO PHE PHE TYR SEQRES 5 B 178 PRO VAL ASP TYR GLY ILE ILE PRO GLN THR TRP TYR ASP SEQRES 6 B 178 ASP GLY ASP PRO PHE ASP ILE MET VAL ILE MET ARG GLU SEQRES 7 B 178 PRO VAL TYR PRO LEU THR ILE ILE GLU ALA ARG PRO ILE SEQRES 8 B 178 GLY ILE MET LYS MET GLU ASP SER GLY ASP LYS ASP TRP SEQRES 9 B 178 LYS VAL LEU ALA VAL PRO VAL GLU ASP PRO TYR PHE ASN SEQRES 10 B 178 ASP TRP LYS ASP ILE SER ASP VAL PRO LYS ALA PHE LEU SEQRES 11 B 178 ASP GLU ILE ALA HIS PHE PHE GLN ARG TYR LYS GLU LEU SEQRES 12 B 178 GLN GLY LYS THR THR LYS ILE GLU GLY TRP GLY ASN ALA SEQRES 13 B 178 GLU GLU ALA LYS ARG GLU ILE LEU ARG ALA ILE GLU MET SEQRES 14 B 178 TYR LYS GLU LYS PHE GLY LYS GLU GLU HET MN A 432 1 HET MN B 433 1 HETNAM MN MANGANESE (II) ION FORMUL 3 MN 2(MN 2+) FORMUL 5 HOH *419(H2 O) HELIX 1 1 ASN A 2 LEU A 7 1 6 HELIX 2 2 ASP A 113 ASN A 117 5 5 HELIX 3 3 ASP A 121 VAL A 125 5 5 HELIX 4 4 PRO A 126 TYR A 140 1 15 HELIX 5 5 LYS A 141 GLY A 145 5 5 HELIX 6 6 ALA A 156 PHE A 174 1 19 HELIX 7 7 ASN B 2 LEU B 7 1 6 HELIX 8 8 ASP B 113 ASN B 117 5 5 HELIX 9 9 ASP B 121 VAL B 125 5 5 HELIX 10 10 PRO B 126 TYR B 140 1 15 HELIX 11 11 LYS B 141 GLY B 145 5 5 HELIX 12 12 ASN B 155 PHE B 174 1 20 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 ALA A 108 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 GLU A 151 N LYS A 95 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 SHEET 1 C 7 LYS B 149 GLY B 154 0 SHEET 2 C 7 ILE B 85 GLU B 97 -1 N ILE B 93 O GLY B 154 SHEET 3 C 7 LYS B 105 PRO B 110 -1 O VAL B 109 N ARG B 89 SHEET 4 C 7 ASP B 71 VAL B 74 1 N MET B 73 O VAL B 106 SHEET 5 C 7 ASP B 55 ILE B 58 -1 N ASP B 55 O VAL B 74 SHEET 6 C 7 VAL B 17 ILE B 23 -1 N LEU B 20 O ILE B 58 SHEET 7 C 7 ILE B 85 GLU B 97 -1 O ALA B 88 N VAL B 17 SHEET 1 D 2 ASN B 29 LEU B 33 0 SHEET 2 D 2 LEU B 40 VAL B 45 -1 O ARG B 44 N LYS B 30 LINK OD2 ASP A 66 MN MN A 432 1555 1555 2.20 LINK OD2AASP A 71 MN MN A 432 1555 1555 2.19 LINK OD1BASP A 71 MN MN A 432 1555 1555 2.25 LINK OD1 ASP A 103 MN MN A 432 1555 1555 2.12 LINK O HOH A 225 MN MN A 432 1555 1555 2.17 LINK O BHOH A 235 MN MN A 432 1555 1555 1.99 LINK O AHOH A 235 MN MN A 432 1555 1555 2.18 LINK O HOH A 263 MN MN A 432 1555 1555 2.22 LINK OD2 ASP B 66 MN MN B 433 1555 1555 2.19 LINK OD1 ASP B 71 MN MN B 433 1555 1555 2.14 LINK OD1 ASP B 103 MN MN B 433 1555 1555 2.16 LINK O HOH B 226 MN MN B 433 1555 1555 2.16 LINK O HOH B 236 MN MN B 433 1555 1555 2.16 LINK O HOH B 264 MN MN B 433 1555 1555 2.21 CISPEP 1 VAL A 13 PRO A 14 0 -1.68 CISPEP 2 VAL B 13 PRO B 14 0 -3.05 CISPEP 3 VAL B 13 PRO B 14 0 -4.86 SITE 1 AC1 6 ASP A 66 ASP A 71 ASP A 103 HOH A 225 SITE 2 AC1 6 HOH A 235 HOH A 263 SITE 1 AC2 6 ASP B 66 ASP B 71 ASP B 103 HOH B 226 SITE 2 AC2 6 HOH B 236 HOH B 264 CRYST1 114.514 114.514 148.438 90.00 90.00 120.00 H 3 2 36 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 0.008733 0.005042 0.000000 0.00000 SCALE2 0.000000 0.010083 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006737 0.00000