HEADER HYDROLASE 28-NOV-03 1RMQ TITLE CRYSTAL STRUCTURE OF APHA CLASS B ACID PHOSPHATASE/PHOSPHOTRANSFERASE TITLE 2 WITH OSMIATE MIMICKING THE CATALYTIC INTERMEDIATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLASS B ACID PHOSPHATASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.3.2; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: APHA, NAPA, B4055, SF4149, S3580; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH5ALPHA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PATAC KEYWDS CLASS B ACID PHOSPHATASE, DDDD ACID PHOSPHATASE, METALLO-ENZYME, KEYWDS 2 OSMIATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.CALDERONE,C.FORLEO,M.BENVENUTI,G.M.ROSSOLINI,M.C.THALLER,S.MANGANI REVDAT 4 23-AUG-23 1RMQ 1 REMARK LINK REVDAT 3 13-JUL-11 1RMQ 1 VERSN REVDAT 2 24-FEB-09 1RMQ 1 VERSN REVDAT 1 14-DEC-04 1RMQ 0 JRNL AUTH V.CALDERONE,C.FORLEO,M.BENVENUTI,G.M.ROSSOLINI,M.C.THALLER, JRNL AUTH 2 S.MANGANI JRNL TITL INSIGHTS IN THE CATALYTIC MECHANISM OF APHA FROM ESCHERICHIA JRNL TITL 2 COLI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.C.THALLER,S.SCHIPPA,A.BONCI,S.CRESTI,G.M.ROSSOLINI REMARK 1 TITL IDENTIFICATION OF THE GENE (APHA) ENCODING THE CLASS B ACID REMARK 1 TITL 2 PHOSPHATASE/PHOSPHOTRANSFERASE OF ESCHERICHIA COLI MG1655 REMARK 1 TITL 3 AND CHARACTERIZATION OF ITS PRODUCT REMARK 1 REF FEMS MICROBIOL.LETT. V. 146 191 1997 REMARK 1 REFN ISSN 0378-1097 REMARK 1 DOI 10.1016/S0378-1097(96)00474-0 REMARK 1 REFERENCE 2 REMARK 1 AUTH C.FORLEO,M.BENVENUTI,V.CALDERONE,S.SCHIPPA,J.D.DOCQUIER, REMARK 1 AUTH 2 M.C.THALLER,G.M ROSSOLINI,S.MANGANI REMARK 1 TITL EXPRESSION, PURIFICATION, CRYSTALLIZATION AND PRELIMINARY REMARK 1 TITL 2 X-RAY CHARACTERIZATION OF THE CLASS B ACID PHOSPHATASE REMARK 1 TITL 3 (APHA) FROM ESCHERICHIA COLI REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 59 1058 2003 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444903006826 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 29421 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2265 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2101 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE SET COUNT : 163 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3282 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 296 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.50000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.58000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.183 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.165 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.113 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.040 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3353 ; 0.026 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4548 ; 1.943 ; 1.929 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 415 ; 8.202 ; 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): 483 ; 0.148 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2616 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1640 ; 0.222 ; 0.200 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): 284 ; 0.213 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.324 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 116 ; 0.252 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 28 ; 0.250 ; 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): 2082 ; 1.135 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3365 ; 1.853 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1271 ; 3.316 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1183 ; 5.066 ; 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 : NULL 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: NULL REMARK 4 REMARK 4 1RMQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000020888. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.13980, 1.14057, 1.13800 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31710 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : 0.08900 REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.40200 REMARK 200 R SYM FOR SHELL (I) : 0.40200 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1N8N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: APHA 6MG/ML, 50MM NA ACETATE, 25% PEG REMARK 280 6000, 10MM OSMIATE, PH 7.2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 45.86600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.22350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.86600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.22350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: THE BIOLOGICAL ASSEMBLY IS A TETRAMER, BUT THERE IS A DIMER REMARK 300 IN THE ASYMMETRIC UNIT. 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 13870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32980 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -165.0 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 -1.000000 0.000000 0.000000 -47.54795 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 78.20264 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 513 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 540 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 SER A 1 REMARK 465 SER A 2 REMARK 465 PRO A 3 REMARK 465 SER B 1 REMARK 465 SER B 2 REMARK 465 PRO B 3 REMARK 465 SER B 4 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASN A 170 OD1 REMARK 480 PRO B 5 CD REMARK 480 LEU B 6 CD1 REMARK 480 PRO B 8 CB REMARK 480 GLU B 17 OE2 REMARK 480 ASP B 69 CB CG OD2 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 THR A 151 C THR A 151 O -0.155 REMARK 500 PRO B 5 CD PRO B 5 N -0.095 REMARK 500 GLU B 17 CD GLU B 17 OE2 -0.152 REMARK 500 ALA B 27 CA ALA B 27 CB 0.129 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 14 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 44 CB - CG - OD2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ASP A 106 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 145 N - CA - C ANGL. DEV. = 17.1 DEGREES REMARK 500 ARG A 181 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG A 181 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 GLU B 17 OE1 - CD - OE2 ANGL. DEV. = -16.2 DEGREES REMARK 500 GLU B 17 CG - CD - OE2 ANGL. DEV. = 12.8 DEGREES REMARK 500 ASP B 44 CB - CG - OD2 ANGL. DEV. = 8.6 DEGREES REMARK 500 ASP B 47 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 69 N - CA - CB ANGL. DEV. = 12.1 DEGREES REMARK 500 ASP B 69 OD1 - CG - OD2 ANGL. DEV. = 15.6 DEGREES REMARK 500 ASP B 69 CB - CG - OD1 ANGL. DEV. = -11.1 DEGREES REMARK 500 ASP B 69 CB - CG - OD2 ANGL. DEV. = -7.6 DEGREES REMARK 500 GLU B 78 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 MET B 100 CG - SD - CE ANGL. DEV. = -14.2 DEGREES REMARK 500 ARG B 103 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ASP B 158 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP B 171 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG B 181 NE - CZ - NH1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG B 181 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG B 184 NE - CZ - NH2 ANGL. DEV. = -3.2 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 PRO A 38 137.34 -39.37 REMARK 500 SER A 64 63.13 -160.64 REMARK 500 SER A 67 -173.07 -174.60 REMARK 500 LYS A 146 90.13 -167.42 REMARK 500 ALA B 34 120.93 -32.24 REMARK 500 ILE B 45 -61.24 -90.26 REMARK 500 SER B 64 66.26 -165.83 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 GLY A 144 ASP A 145 103.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 HOH A 546 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 CO A 401 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 44 OD2 REMARK 620 2 ASP A 46 O 90.7 REMARK 620 3 ASP A 167 OD1 85.9 88.2 REMARK 620 4 HOH A 408 O 84.8 172.2 85.2 REMARK 620 5 HOH A 428 O 179.6 89.6 94.2 94.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO B 403 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 44 OD2 REMARK 620 2 ASP B 46 O 87.6 REMARK 620 3 ASP B 167 OD1 85.8 88.5 REMARK 620 4 HOH B 495 O 88.8 168.5 80.3 REMARK 620 5 HOH B 551 O 174.4 87.5 91.4 95.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 OS B 404 OS REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 44 OD1 REMARK 620 2 HOH B 549 O 76.1 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OS A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OS B 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OS A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OS B 406 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1N8N RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE AU3+ COMPLEX OF APHA CLASS B ACID REMARK 900 PHOSPHATASE/PHOSPHOTRANSFERASE FROM E. COLI AT 1.7 A RESOLUTION REMARK 900 RELATED ID: 1N9K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE BROMIDE ADDUCT OF APHA CLASS B ACID REMARK 900 PHOSPHATASE/PHOSPHOTRANSFERASE FROM E. COLI AT 2.2 A RESOLUTION REMARK 900 RELATED ID: 1RM7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF APHA CLASS B ACID PHOSPHATASE/ REMARK 900 PHOSPHOTRANSFERASE TERNARY COMPLEX WITH ADENOSINE AND PHOSPHATE AT REMARK 900 2 A RESOLUTION REMARK 900 RELATED ID: 1RMT RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF APHA CLASS B ACID PHOSPHATASE/ REMARK 900 PHOSPHOTRANSFERASE COMPLEXED WITH ADENOSINE REMARK 900 RELATED ID: 1RMW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF APHA CLASS B ACID PHOSPHATASE/ REMARK 900 PHOSPHOTRANSFERASE TERNARY COMPLEX WITH ADENOSINE AND PHOSPHATE REMARK 900 BOUND TO THE CATALYTIC METAL AT 1.2 A RESOLUTION REMARK 900 RELATED ID: 1RMY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF APHA CLASS B ACID PHOSPHATASE/ REMARK 900 PHOSPHOTRANSFERASE TERNARY COMPLEX WITH DEOXYCYTOSINE AND PHOSPHATE REMARK 900 BOUND TO THE CATALYTIC METAL DBREF 1RMQ A 1 212 UNP P32697 APHA_ECOLI 26 237 DBREF 1RMQ B 1 212 UNP P32697 APHA_ECOLI 26 237 SEQRES 1 A 212 SER SER PRO SER PRO LEU ASN PRO GLY THR ASN VAL ALA SEQRES 2 A 212 ARG LEU ALA GLU GLN ALA PRO ILE HIS TRP VAL SER VAL SEQRES 3 A 212 ALA GLN ILE GLU ASN SER LEU ALA GLY ARG PRO PRO MET SEQRES 4 A 212 ALA VAL GLY PHE ASP ILE ASP ASP THR VAL LEU PHE SER SEQRES 5 A 212 SER PRO GLY PHE TRP ARG GLY LYS LYS THR PHE SER PRO SEQRES 6 A 212 GLU SER GLU ASP TYR LEU LYS ASN PRO VAL PHE TRP GLU SEQRES 7 A 212 LYS MET ASN ASN GLY TRP ASP GLU PHE SER ILE PRO LYS SEQRES 8 A 212 GLU VAL ALA ARG GLN LEU ILE ASP MET HIS VAL ARG ARG SEQRES 9 A 212 GLY ASP ALA ILE PHE PHE VAL THR GLY ARG SER PRO THR SEQRES 10 A 212 LYS THR GLU THR VAL SER LYS THR LEU ALA ASP ASN PHE SEQRES 11 A 212 HIS ILE PRO ALA THR ASN MET ASN PRO VAL ILE PHE ALA SEQRES 12 A 212 GLY ASP LYS PRO GLY GLN ASN THR LYS SER GLN TRP LEU SEQRES 13 A 212 GLN ASP LYS ASN ILE ARG ILE PHE TYR GLY ASP SER ASP SEQRES 14 A 212 ASN ASP ILE THR ALA ALA ARG ASP VAL GLY ALA ARG GLY SEQRES 15 A 212 ILE ARG ILE LEU ARG ALA SER ASN SER THR TYR LYS PRO SEQRES 16 A 212 LEU PRO GLN ALA GLY ALA PHE GLY GLU GLU VAL ILE VAL SEQRES 17 A 212 ASN SER GLU TYR SEQRES 1 B 212 SER SER PRO SER PRO LEU ASN PRO GLY THR ASN VAL ALA SEQRES 2 B 212 ARG LEU ALA GLU GLN ALA PRO ILE HIS TRP VAL SER VAL SEQRES 3 B 212 ALA GLN ILE GLU ASN SER LEU ALA GLY ARG PRO PRO MET SEQRES 4 B 212 ALA VAL GLY PHE ASP ILE ASP ASP THR VAL LEU PHE SER SEQRES 5 B 212 SER PRO GLY PHE TRP ARG GLY LYS LYS THR PHE SER PRO SEQRES 6 B 212 GLU SER GLU ASP TYR LEU LYS ASN PRO VAL PHE TRP GLU SEQRES 7 B 212 LYS MET ASN ASN GLY TRP ASP GLU PHE SER ILE PRO LYS SEQRES 8 B 212 GLU VAL ALA ARG GLN LEU ILE ASP MET HIS VAL ARG ARG SEQRES 9 B 212 GLY ASP ALA ILE PHE PHE VAL THR GLY ARG SER PRO THR SEQRES 10 B 212 LYS THR GLU THR VAL SER LYS THR LEU ALA ASP ASN PHE SEQRES 11 B 212 HIS ILE PRO ALA THR ASN MET ASN PRO VAL ILE PHE ALA SEQRES 12 B 212 GLY ASP LYS PRO GLY GLN ASN THR LYS SER GLN TRP LEU SEQRES 13 B 212 GLN ASP LYS ASN ILE ARG ILE PHE TYR GLY ASP SER ASP SEQRES 14 B 212 ASN ASP ILE THR ALA ALA ARG ASP VAL GLY ALA ARG GLY SEQRES 15 B 212 ILE ARG ILE LEU ARG ALA SER ASN SER THR TYR LYS PRO SEQRES 16 B 212 LEU PRO GLN ALA GLY ALA PHE GLY GLU GLU VAL ILE VAL SEQRES 17 B 212 ASN SER GLU TYR HET CO A 401 1 HET OS A 402 1 HET OS A 405 1 HET CO B 403 1 HET OS B 404 1 HET OS B 406 1 HETNAM CO COBALT (II) ION HETNAM OS OSMIUM ION FORMUL 3 CO 2(CO 2+) FORMUL 4 OS 4(OS 3+) FORMUL 9 HOH *296(H2 O) HELIX 1 1 ASN A 11 GLU A 17 1 7 HELIX 2 2 SER A 25 LEU A 33 1 9 HELIX 3 3 SER A 52 SER A 64 1 13 HELIX 4 4 GLU A 68 LYS A 72 5 5 HELIX 5 5 ASN A 73 ASN A 81 1 9 HELIX 6 6 GLY A 83 SER A 88 5 6 HELIX 7 7 LYS A 91 GLY A 105 1 15 HELIX 8 8 THR A 121 HIS A 131 1 11 HELIX 9 9 LYS A 152 ASN A 160 1 9 HELIX 10 10 SER A 168 VAL A 178 1 11 HELIX 11 11 ASN B 11 GLU B 17 1 7 HELIX 12 12 SER B 25 ALA B 34 1 10 HELIX 13 13 SER B 52 SER B 64 1 13 HELIX 14 14 GLU B 68 LYS B 72 5 5 HELIX 15 15 ASN B 73 ASN B 81 1 9 HELIX 16 16 GLY B 83 SER B 88 5 6 HELIX 17 17 LYS B 91 ARG B 104 1 14 HELIX 18 18 THR B 121 HIS B 131 1 11 HELIX 19 19 THR B 151 ASN B 160 1 10 HELIX 20 20 SER B 168 VAL B 178 1 11 SHEET 1 A 7 HIS A 22 VAL A 24 0 SHEET 2 A 7 GLU A 205 ILE A 207 1 O VAL A 206 N HIS A 22 SHEET 3 A 7 ARG A 181 ARG A 184 1 N ARG A 184 O ILE A 207 SHEET 4 A 7 ILE A 161 GLY A 166 1 N PHE A 164 O ILE A 183 SHEET 5 A 7 ALA A 40 PHE A 43 1 N GLY A 42 O ILE A 163 SHEET 6 A 7 ALA A 107 THR A 112 1 O ALA A 107 N VAL A 41 SHEET 7 A 7 ILE A 141 PHE A 142 1 O ILE A 141 N THR A 112 SHEET 1 B 2 LEU A 50 PHE A 51 0 SHEET 2 B 2 ILE A 89 PRO A 90 -1 O ILE A 89 N PHE A 51 SHEET 1 C 2 HIS B 22 VAL B 24 0 SHEET 2 C 2 GLU B 205 ILE B 207 1 O VAL B 206 N HIS B 22 SHEET 1 D 5 ILE B 141 PHE B 142 0 SHEET 2 D 5 ALA B 107 THR B 112 1 N THR B 112 O ILE B 141 SHEET 3 D 5 ALA B 40 PHE B 43 1 N VAL B 41 O ALA B 107 SHEET 4 D 5 ILE B 161 GLY B 166 1 O ILE B 163 N GLY B 42 SHEET 5 D 5 ARG B 181 ARG B 184 1 O ILE B 183 N PHE B 164 SHEET 1 E 2 LEU B 50 PHE B 51 0 SHEET 2 E 2 ILE B 89 PRO B 90 -1 O ILE B 89 N PHE B 51 LINK NE2 HIS A 22 OS OS A 405 1555 1555 2.24 LINK OD2 ASP A 44 CO CO A 401 1555 1555 2.07 LINK O ASP A 46 CO CO A 401 1555 1555 2.19 LINK OD1 ASP A 167 CO CO A 401 1555 1555 2.13 LINK CO CO A 401 O HOH A 408 1555 1555 2.11 LINK CO CO A 401 O HOH A 428 1555 1555 2.20 LINK OD2 ASP B 44 CO CO B 403 1555 1555 1.96 LINK OD1 ASP B 44 OS OS B 404 1555 1555 2.32 LINK O ASP B 46 CO CO B 403 1555 1555 2.17 LINK OD1 ASP B 167 CO CO B 403 1555 1555 2.11 LINK CO CO B 403 O HOH B 495 1555 1555 2.04 LINK CO CO B 403 O HOH B 551 1555 1555 2.12 LINK OS OS B 404 O HOH B 549 1555 1555 2.35 CISPEP 1 PRO A 147 GLY A 148 0 -15.02 CISPEP 2 LYS A 194 PRO A 195 0 3.75 CISPEP 3 LYS B 194 PRO B 195 0 -1.26 SITE 1 AC1 6 ASP A 44 ASP A 46 ASP A 167 OS A 402 SITE 2 AC1 6 HOH A 408 HOH A 428 SITE 1 AC2 3 ASP A 44 CO A 401 HOH A 442 SITE 1 AC3 6 ASP B 44 ASP B 46 ASP B 167 OS B 404 SITE 2 AC3 6 HOH B 495 HOH B 551 SITE 1 AC4 5 ASP B 44 CO B 403 HOH B 442 HOH B 548 SITE 2 AC4 5 HOH B 549 SITE 1 AC5 1 HIS A 22 SITE 1 AC6 1 HIS B 22 CRYST1 91.732 66.447 91.523 90.00 121.30 90.00 C 1 2 1 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 0.010901 0.000000 0.006628 0.00000 SCALE2 0.000000 0.015050 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012787 0.00000