HEADER HYDROLASE 16-JUN-03 1OIE TITLE 5'-NUCLEOTIDASE (E. COLI) WITH AN ENGINEERED DISULFIDE BRIDGE (S228C, TITLE 2 P513C) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN USHA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UDP-SUGAR DIPHOSPHATASE, UDP-SUGAR PYROPHOSPHATASE, 5'- COMPND 5 NUCLEOTIDASE; COMPND 6 EC: 3.1.3.5, 3.6.1.45; COMPND 7 ENGINEERED: YES; COMPND 8 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: ER2566; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 8 OTHER_DETAILS: DISULFIDE CROSSLINK BETWEEN N- AND C-TERMINAL DOMAINS KEYWDS METALLOPROTEIN, HYDROLASE, DOMAIN MOVEMENT, DISULFIDE ENGINEERING, KEYWDS 2 CONFORMATIONAL TRAPPING, PERIPLASMIC EXPDTA X-RAY DIFFRACTION AUTHOR R.SCHULTZ-HEIENBROK,T.MAIER,N.STRAETER REVDAT 4 13-DEC-23 1OIE 1 REMARK LINK REVDAT 3 13-JUL-11 1OIE 1 VERSN REVDAT 2 24-FEB-09 1OIE 1 VERSN REVDAT 1 05-AUG-04 1OIE 0 JRNL AUTH R.SCHULTZ-HEIENBROK,T.MAIER,N.STRAETER JRNL TITL TRAPPING A 96 DEGREE DOMAIN ROTATION IN TWO DISTINCT JRNL TITL 2 CONFORMATIONS BY ENGINEERED DISULFIDE BRIDGES JRNL REF PROTEIN SCI. V. 13 1811 2004 JRNL REFN ISSN 0961-8368 JRNL PMID 15215524 JRNL DOI 10.1110/PS.04629604 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH T.KNOEFEL,N.STRAETER REMARK 1 TITL E. COLI 5'-NUCLEOTIDASE UNDERGOES A HINGE-BENDING DOMAIN REMARK 1 TITL 2 ROTATION RESEMBLING A BALL-AND-SOCKET MOTION REMARK 1 REF J.MOL.BIOL. V. 309 255 2001 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 11491294 REMARK 1 DOI 10.1006/JMBI.2001.4657 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.KNOEFEL,N.STRAETER REMARK 1 TITL X-RAY STRUCTURE OF THE ESCHERICHIA COLI PERIPLASMIC REMARK 1 TITL 2 5'-NUCLEOTIDASE CONTAINING A DIMETAL CATALYTIC SITE REMARK 1 REF NAT.STRUCT.BIOL. V. 6 448 1999 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 10331872 REMARK 1 DOI 10.1038/8253 REMARK 2 REMARK 2 RESOLUTION. 2.33 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.19 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) : 2.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 74.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 26420 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1391 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) : 2.33 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.39 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1933 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1540 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.2550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4048 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 389 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.40000 REMARK 3 B22 (A**2) : -0.40000 REMARK 3 B33 (A**2) : 0.80000 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): 0.286 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.214 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.131 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.303 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4134 ; 0.024 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3672 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5592 ; 1.742 ; 1.953 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8598 ; 0.872 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 517 ; 6.628 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 599 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4653 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 792 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 891 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4610 ; 0.253 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2489 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 347 ; 0.188 ; 0.200 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): 17 ; 0.263 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 67 ; 0.254 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 19 ; 0.116 ; 0.200 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): 2571 ; 0.934 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4126 ; 1.685 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1563 ; 2.575 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1466 ; 4.119 ; 4.500 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 : 2 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 26 A 340 REMARK 3 ORIGIN FOR THE GROUP (A): 50.0900 -3.6842 15.9923 REMARK 3 T TENSOR REMARK 3 T11: 0.0301 T22: 0.0388 REMARK 3 T33: 0.0111 T12: 0.0243 REMARK 3 T13: 0.0055 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.4116 L22: 0.2225 REMARK 3 L33: 0.3327 L12: -0.0717 REMARK 3 L13: 0.2691 L23: -0.0026 REMARK 3 S TENSOR REMARK 3 S11: 0.0325 S12: 0.0658 S13: 0.0028 REMARK 3 S21: 0.0074 S22: 0.0004 S23: -0.0090 REMARK 3 S31: 0.0532 S32: 0.0560 S33: -0.0329 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 360 A 550 REMARK 3 ORIGIN FOR THE GROUP (A): 32.3292 24.6893 24.5535 REMARK 3 T TENSOR REMARK 3 T11: 0.0286 T22: 0.0108 REMARK 3 T33: 0.0439 T12: 0.0003 REMARK 3 T13: 0.0005 T23: 0.0016 REMARK 3 L TENSOR REMARK 3 L11: 0.6628 L22: 0.3137 REMARK 3 L33: 0.1095 L12: 0.0459 REMARK 3 L13: -0.1261 L23: -0.0317 REMARK 3 S TENSOR REMARK 3 S11: -0.0152 S12: -0.0014 S13: 0.0537 REMARK 3 S21: -0.0018 S22: -0.0038 S23: 0.0112 REMARK 3 S31: -0.0004 S32: 0.0058 S33: 0.0190 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 1OIE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1290012908. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54179 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 193519 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.330 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.960 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.84 REMARK 200 R MERGE FOR SHELL (I) : 0.16500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 11.80 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: PDB ENTRY 1HP1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.1 MALONATE PH 6.5, PH 6.50 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 90.33200 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.56600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.56600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.16600 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.56600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.56600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 135.49800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.56600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.56600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.16600 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.56600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.56600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 135.49800 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 90.33200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 400 REMARK 400 COMPOUND REMARK 400 CHAIN A ENGINEERED MUTATION SER 228 CYS, PRO 513 CYS 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 THR A 324 REMARK 465 TRP A 325 REMARK 465 GLU A 326 REMARK 465 ASP A 327 REMARK 465 GLY A 328 REMARK 465 LYS A 329 REMARK 465 HIS A 552 REMARK 465 HIS A 553 REMARK 465 HIS A 554 REMARK 465 HIS A 555 REMARK 465 HIS A 556 REMARK 465 HIS A 557 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 551 CA C O CB CG CD OE1 REMARK 470 GLU A 551 OE2 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 HOH A 2047 O HOH A 2083 2.18 REMARK 500 O HOH A 2193 O HOH A 2196 2.19 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 MET A 218 SD MET A 218 CE -0.366 REMARK 500 MET A 259 SD MET A 259 CE -0.345 REMARK 500 MET A 438 SD MET A 438 CE -0.371 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 TYR A 26 N - CA - C ANGL. DEV. = -32.9 DEGREES REMARK 500 GLU A 27 N - CA - CB ANGL. DEV. = -14.6 DEGREES REMARK 500 ASP A 110 CB - CG - OD2 ANGL. DEV. = 9.2 DEGREES REMARK 500 ASP A 222 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 268 CB - CG - OD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 370 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 370 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 437 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 522 CB - CG - OD1 ANGL. DEV. = 6.2 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 TYR A 54 -145.48 36.79 REMARK 500 ASP A 84 62.04 60.70 REMARK 500 THR A 87 110.49 82.95 REMARK 500 GLN A 161 -115.53 76.58 REMARK 500 TYR A 183 56.33 -109.55 REMARK 500 HIS A 252 -56.57 81.38 REMARK 500 GLN A 254 65.53 65.13 REMARK 500 HIS A 289 -95.39 69.17 REMARK 500 THR A 495 -154.34 -163.83 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 NI A 700 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 84 OD2 REMARK 620 2 ASN A 116 OD1 91.3 REMARK 620 3 HIS A 217 NE2 85.4 90.4 REMARK 620 4 HIS A 252 ND1 166.7 101.7 97.4 REMARK 620 5 HOH A2047 O 79.3 125.7 140.7 90.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI A 700 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HO5 RELATED DB: PDB REMARK 900 5'-NUCLEOTIDASE (E. COLI) IN COMPLEX WITH ADENOSINE ANDPHOSPHATE REMARK 900 RELATED ID: 1HP1 RELATED DB: PDB REMARK 900 5'-NUCLEOTIDASE (OPEN FORM) COMPLEX WITH ATP REMARK 900 RELATED ID: 1HPU RELATED DB: PDB REMARK 900 5'-NUCLEOTIDASE (CLOSED FORM), COMPLEX WITH AMPCP REMARK 900 RELATED ID: 1OI8 RELATED DB: PDB REMARK 900 5'-NUCLEOTIDASE (E. COLI) WITH AN ENGINEERED DISULFIDE BRIDGE (P90C, REMARK 900 L424C) REMARK 900 RELATED ID: 1OID RELATED DB: PDB REMARK 900 5'-NUCLEOTIDASE (E. COLI) WITH AN ENGINEERED DISULFIDE BRIDGE REMARK 900 (S228C, P513C) REMARK 900 RELATED ID: 1USH RELATED DB: PDB REMARK 900 5'-NUCLEOTIDASE FROM E. COLI REMARK 900 RELATED ID: 2USH RELATED DB: PDB REMARK 900 5'-NUCLEOTIDASE FROM E. COLI REMARK 999 REMARK 999 SEQUENCE REMARK 999 ADDITIONAL GLU AND 6X HIS AT C-TERMINUS DBREF 1OIE A 26 550 UNP P07024 USHA_ECOLI 26 550 DBREF 1OIE A 551 557 PDB 1OIE 1OIE 551 557 SEQADV 1OIE CYS A 228 UNP P10725 SER 228 ENGINEERED MUTATION SEQADV 1OIE CYS A 513 UNP P10725 PRO 513 ENGINEERED MUTATION SEQRES 1 A 532 TYR GLU GLN ASP LYS THR TYR LYS ILE THR VAL LEU HIS SEQRES 2 A 532 THR ASN ASP HIS HIS GLY HIS PHE TRP ARG ASN GLU TYR SEQRES 3 A 532 GLY GLU TYR GLY LEU ALA ALA GLN LYS THR LEU VAL ASP SEQRES 4 A 532 GLY ILE ARG LYS GLU VAL ALA ALA GLU GLY GLY SER VAL SEQRES 5 A 532 LEU LEU LEU SER GLY GLY ASP ILE ASN THR GLY VAL PRO SEQRES 6 A 532 GLU SER ASP LEU GLN ASP ALA GLU PRO ASP PHE ARG GLY SEQRES 7 A 532 MET ASN LEU VAL GLY TYR ASP ALA MET ALA ILE GLY ASN SEQRES 8 A 532 HIS GLU PHE ASP ASN PRO LEU THR VAL LEU ARG GLN GLN SEQRES 9 A 532 GLU LYS TRP ALA LYS PHE PRO LEU LEU SER ALA ASN ILE SEQRES 10 A 532 TYR GLN LYS SER THR GLY GLU ARG LEU PHE LYS PRO TRP SEQRES 11 A 532 ALA LEU PHE LYS ARG GLN ASP LEU LYS ILE ALA VAL ILE SEQRES 12 A 532 GLY LEU THR THR ASP ASP THR ALA LYS ILE GLY ASN PRO SEQRES 13 A 532 GLU TYR PHE THR ASP ILE GLU PHE ARG LYS PRO ALA ASP SEQRES 14 A 532 GLU ALA LYS LEU VAL ILE GLN GLU LEU GLN GLN THR GLU SEQRES 15 A 532 LYS PRO ASP ILE ILE ILE ALA ALA THR HIS MET GLY HIS SEQRES 16 A 532 TYR ASP ASN GLY GLU HIS GLY CYS ASN ALA PRO GLY ASP SEQRES 17 A 532 VAL GLU MET ALA ARG ALA LEU PRO ALA GLY SER LEU ALA SEQRES 18 A 532 MET ILE VAL GLY GLY HIS SER GLN ASP PRO VAL CYS MET SEQRES 19 A 532 ALA ALA GLU ASN LYS LYS GLN VAL ASP TYR VAL PRO GLY SEQRES 20 A 532 THR PRO CYS LYS PRO ASP GLN GLN ASN GLY ILE TRP ILE SEQRES 21 A 532 VAL GLN ALA HIS GLU TRP GLY LYS TYR VAL GLY ARG ALA SEQRES 22 A 532 ASP PHE GLU PHE ARG ASN GLY GLU MET LYS MET VAL ASN SEQRES 23 A 532 TYR GLN LEU ILE PRO VAL ASN LEU LYS LYS LYS VAL THR SEQRES 24 A 532 TRP GLU ASP GLY LYS SER GLU ARG VAL LEU TYR THR PRO SEQRES 25 A 532 GLU ILE ALA GLU ASN GLN GLN MET ILE SER LEU LEU SER SEQRES 26 A 532 PRO PHE GLN ASN LYS GLY LYS ALA GLN LEU GLU VAL LYS SEQRES 27 A 532 ILE GLY GLU THR ASN GLY ARG LEU GLU GLY ASP ARG ASP SEQRES 28 A 532 LYS VAL ARG PHE VAL GLN THR ASN MET GLY ARG LEU ILE SEQRES 29 A 532 LEU ALA ALA GLN MET ASP ARG THR GLY ALA ASP PHE ALA SEQRES 30 A 532 VAL MET SER GLY GLY GLY ILE ARG ASP SER ILE GLU ALA SEQRES 31 A 532 GLY ASP ILE SER TYR LYS ASN VAL LEU LYS VAL GLN PRO SEQRES 32 A 532 PHE GLY ASN VAL VAL VAL TYR ALA ASP MET THR GLY LYS SEQRES 33 A 532 GLU VAL ILE ASP TYR LEU THR ALA VAL ALA GLN MET LYS SEQRES 34 A 532 PRO ASP SER GLY ALA TYR PRO GLN PHE ALA ASN VAL SER SEQRES 35 A 532 PHE VAL ALA LYS ASP GLY LYS LEU ASN ASP LEU LYS ILE SEQRES 36 A 532 LYS GLY GLU PRO VAL ASP PRO ALA LYS THR TYR ARG MET SEQRES 37 A 532 ALA THR LEU ASN PHE ASN ALA THR GLY GLY ASP GLY TYR SEQRES 38 A 532 PRO ARG LEU ASP ASN LYS CYS GLY TYR VAL ASN THR GLY SEQRES 39 A 532 PHE ILE ASP ALA GLU VAL LEU LYS ALA TYR ILE GLN LYS SEQRES 40 A 532 SER SER PRO LEU ASP VAL SER VAL TYR GLU PRO LYS GLY SEQRES 41 A 532 GLU VAL SER TRP GLN GLU HIS HIS HIS HIS HIS HIS HET NI A 700 1 HETNAM NI NICKEL (II) ION FORMUL 2 NI NI 2+ FORMUL 3 HOH *389(H2 O) HELIX 1 1 GLY A 55 GLU A 73 1 19 HELIX 2 2 VAL A 89 LEU A 94 1 6 HELIX 3 3 ALA A 97 GLY A 108 1 12 HELIX 4 4 GLY A 115 ASP A 120 5 6 HELIX 5 5 PRO A 122 ALA A 133 1 12 HELIX 6 6 ASP A 174 ILE A 178 5 5 HELIX 7 7 LYS A 191 LYS A 208 1 18 HELIX 8 8 TYR A 221 GLU A 225 5 5 HELIX 9 9 GLY A 232 LEU A 240 1 9 HELIX 10 10 ASN A 342 LEU A 360 1 19 HELIX 11 11 ASP A 374 ARG A 379 1 6 HELIX 12 12 THR A 383 GLY A 398 1 16 HELIX 13 13 GLY A 407 ILE A 409 5 3 HELIX 14 14 TYR A 420 GLN A 427 1 8 HELIX 15 15 GLY A 440 ALA A 451 1 12 HELIX 16 16 ASN A 497 THR A 501 1 5 HELIX 17 17 GLY A 502 TYR A 506 5 5 HELIX 18 18 ASP A 522 SER A 534 1 13 HELIX 19 19 ASP A 537 GLU A 542 5 6 SHEET 1 AA 6 LEU A 137 LEU A 138 0 SHEET 2 AA 6 ALA A 111 ALA A 113 1 O MET A 112 N LEU A 138 SHEET 3 AA 6 SER A 76 SER A 81 1 O SER A 81 N ALA A 113 SHEET 4 AA 6 THR A 31 THR A 39 1 O LYS A 33 N SER A 76 SHEET 5 AA 6 TYR A 294 ARG A 303 -1 O GLY A 296 N HIS A 38 SHEET 6 AA 6 GLU A 306 PRO A 316 -1 O GLU A 306 N ARG A 303 SHEET 1 AB 2 ILE A 142 GLN A 144 0 SHEET 2 AB 2 ILE A 187 PHE A 189 -1 O GLU A 188 N TYR A 143 SHEET 1 AC 6 TRP A 155 ARG A 160 0 SHEET 2 AC 6 LEU A 163 THR A 171 -1 O LEU A 163 N ARG A 160 SHEET 3 AC 6 ILE A 211 HIS A 217 1 O ILE A 211 N ALA A 166 SHEET 4 AC 6 MET A 247 VAL A 249 1 O MET A 247 N ALA A 214 SHEET 5 AC 6 ILE A 283 VAL A 286 1 O TRP A 284 N ILE A 248 SHEET 6 AC 6 ASP A 278 GLN A 280 -1 O ASP A 278 N ILE A 285 SHEET 1 AD 2 MET A 259 ALA A 261 0 SHEET 2 AD 2 LYS A 264 LYS A 265 -1 O LYS A 264 N ALA A 260 SHEET 1 AE 2 LYS A 320 LYS A 322 0 SHEET 2 AE 2 ARG A 332 LEU A 334 -1 O VAL A 333 N LYS A 321 SHEET 1 AF 2 LYS A 363 THR A 367 0 SHEET 2 AF 2 GLY A 416 SER A 419 -1 O GLY A 416 N THR A 367 SHEET 1 AG 5 PRO A 461 ALA A 464 0 SHEET 2 AG 5 PHE A 401 SER A 405 -1 O ALA A 402 N ALA A 464 SHEET 3 AG 5 THR A 490 LEU A 496 1 O ALA A 494 N VAL A 403 SHEET 4 AG 5 VAL A 432 THR A 439 -1 O VAL A 434 N THR A 495 SHEET 5 AG 5 TYR A 515 ILE A 521 -1 O VAL A 516 N TYR A 435 SHEET 1 AH 4 GLU A 483 PRO A 484 0 SHEET 2 AH 4 LYS A 474 ILE A 480 -1 O ILE A 480 N GLU A 483 SHEET 3 AH 4 VAL A 466 LYS A 471 -1 O SER A 467 N LYS A 479 SHEET 4 AH 4 VAL A 547 GLN A 550 1 O SER A 548 N ALA A 470 SSBOND 1 CYS A 228 CYS A 513 1555 1555 2.01 SSBOND 2 CYS A 258 CYS A 275 1555 1555 2.04 LINK OD2 ASP A 84 NI NI A 700 1555 1555 2.34 LINK OD1 ASN A 116 NI NI A 700 1555 1555 2.21 LINK NE2 HIS A 217 NI NI A 700 1555 1555 1.96 LINK ND1 HIS A 252 NI NI A 700 1555 1555 2.29 LINK NI NI A 700 O HOH A2047 1555 1555 2.31 CISPEP 1 SER A 534 PRO A 535 0 5.11 SITE 1 AC1 5 ASP A 84 ASN A 116 HIS A 217 HIS A 252 SITE 2 AC1 5 HOH A2047 CRYST1 83.132 83.132 180.664 90.00 90.00 90.00 P 41 21 2 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 0.012029 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005535 0.00000