HEADER HYDROLASE 31-JUL-08 3E0F TITLE CRYSTAL STRUCTURE OF A PUTATIVE METAL-DEPENDENT PHOSPHOESTERASE TITLE 2 (BAD_1165) FROM BIFIDOBACTERIUM ADOLESCENTIS ATCC 15703 AT 2.40 A TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE METAL-DEPENDENT PHOSPHOESTERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BIFIDOBACTERIUM ADOLESCENTIS ATCC 15703; SOURCE 3 ORGANISM_TAXID: 367928; SOURCE 4 ATCC: 15703; SOURCE 5 GENE: YP_910028.1, BAD_1165; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-2, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 8 01-FEB-23 3E0F 1 REMARK SEQADV LINK REVDAT 7 24-JUL-19 3E0F 1 REMARK LINK REVDAT 6 25-OCT-17 3E0F 1 REMARK REVDAT 5 20-JUL-11 3E0F 1 JRNL TITLE REVDAT 4 13-JUL-11 3E0F 1 VERSN REVDAT 3 28-JUL-10 3E0F 1 HEADER TITLE KEYWDS REVDAT 2 24-FEB-09 3E0F 1 VERSN REVDAT 1 02-SEP-08 3E0F 0 JRNL AUTH G.W.HAN,J.KO,C.L.FARR,M.C.DELLER,Q.XU,H.J.CHIU,M.D.MILLER, JRNL AUTH 2 J.SEFCIKOVA,S.SOMAROWTHU,P.J.BEUNING,M.A.ELSLIGER, JRNL AUTH 3 A.M.DEACON,A.GODZIK,S.A.LESLEY,I.A.WILSON,M.J.ONDRECHEN JRNL TITL CRYSTAL STRUCTURE OF A METAL-DEPENDENT PHOSPHOESTERASE JRNL TITL 2 (YP_910028.1) FROM BIFIDOBACTERIUM ADOLESCENTIS: JRNL TITL 3 COMPUTATIONAL PREDICTION AND EXPERIMENTAL VALIDATION OF JRNL TITL 4 PHOSPHOESTERASE ACTIVITY. JRNL REF PROTEINS V. 79 2146 2011 JRNL REFN ISSN 0887-3585 JRNL PMID 21538547 JRNL DOI 10.1002/PROT.23035 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12839 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) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 626 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 906 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.1870 REMARK 3 BIN FREE R VALUE SET COUNT : 44 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2154 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 103 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 36.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.95000 REMARK 3 B22 (A**2) : 0.95000 REMARK 3 B33 (A**2) : -1.43000 REMARK 3 B12 (A**2) : 0.48000 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): 0.326 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.153 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.405 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2269 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1485 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3101 ; 1.470 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3618 ; 0.943 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 297 ; 5.906 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;36.641 ;23.529 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 352 ;15.435 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;20.646 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 351 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2610 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 453 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 489 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1593 ; 0.199 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1135 ; 0.170 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1217 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 115 ; 0.181 ; 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): 19 ; 0.172 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 25 ; 0.180 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.128 ; 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): 1572 ; 2.122 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 594 ; 0.436 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2344 ; 3.087 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 871 ; 5.557 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 757 ; 7.630 ;11.000 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 : 1 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 8 A 293 REMARK 3 ORIGIN FOR THE GROUP (A): 28.9331 28.6887 7.3071 REMARK 3 T TENSOR REMARK 3 T11: -0.0501 T22: -0.0405 REMARK 3 T33: -0.0636 T12: 0.0289 REMARK 3 T13: -0.0170 T23: -0.0057 REMARK 3 L TENSOR REMARK 3 L11: 0.7815 L22: 1.0759 REMARK 3 L33: 0.7446 L12: -0.3269 REMARK 3 L13: -0.0096 L23: 0.3056 REMARK 3 S TENSOR REMARK 3 S11: 0.0423 S12: 0.0296 S13: -0.0728 REMARK 3 S21: -0.0341 S22: -0.0520 S23: 0.0978 REMARK 3 S31: 0.0504 S32: -0.0102 S33: 0.0097 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY REMARK 3 OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 REMARK 3 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL REMARK 3 S-MET INCORPORATION. REMARK 3 (3). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. REMARK 3 (4). THE PRESENCE OF ZINC AND IRON WERE CONFIRMED BY X-RAY REMARK 3 FLUORESCENCE REMARK 3 EXCITATION AND WAVELENGTH SCANS. THE METAL IDENTITY AT THE REMARK 3 INDIVIDUAL REMARK 3 ZN AND FE SITES WAS BASED ON ANOMALOUS DIFFERENCE FOURIER MAP REMARK 3 COMPARISONS REMARK 3 WITH DATA COLLECTED ABOVE AND BELOW THE FOLLOWING K ABSORPTION REMARK 3 EDGES: REMARK 3 FE AND ZN. REMARK 3 (5). AN ACETATE (ACT) ION WAS MODELED BASED ON CRYSTALLIZATION REMARK 3 CONDITION. REMARK 3 (6). PO4 IONS WERE MODELED BASED ON THE ELECTRON DENSITY, REMARK 3 COORDINATION GEOMETRY. REMARK 4 REMARK 4 3E0F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000048717. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(111) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12857 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.579 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.52500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX, SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.0200M CACL2, 30.0000% MPD, 0.1M REMARK 280 ACETATE PH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 36.11333 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 18.05667 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.08500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 9.02833 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 45.14167 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: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 0 REMARK 465 MSE A 1 REMARK 465 SER A 2 REMARK 465 HIS A 3 REMARK 465 VAL A 4 REMARK 465 SER A 5 REMARK 465 TYR A 6 REMARK 465 ALA A 7 REMARK 465 VAL A 294 REMARK 465 GLY A 295 REMARK 465 SER A 296 REMARK 465 SER A 297 REMARK 465 HIS A 298 REMARK 465 ALA A 299 REMARK 465 ALA A 300 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 64 CD OE1 OE2 REMARK 470 GLU A 118 CD OE1 OE2 REMARK 470 GLU A 159 CG CD OE1 OE2 REMARK 470 GLN A 207 CD OE1 NE2 REMARK 470 ARG A 208 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 210 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 250 CD NE CZ NH1 NH2 REMARK 470 LYS A 264 CE NZ REMARK 470 ARG A 293 CG CD NE CZ NH1 NH2 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 OD1 ASP A 224 O ACT A 306 2.11 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 186 CG GLU A 186 CD 0.103 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 109 NE - CZ - NH1 ANGL. DEV. = 3.1 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 SER A 23 -110.14 -137.73 REMARK 500 ALA A 47 52.08 -143.85 REMARK 500 GLU A 80 -121.96 56.79 REMARK 500 ASP A 167 -107.21 -140.14 REMARK 500 HIS A 202 54.28 30.21 REMARK 500 ARG A 208 -61.77 86.10 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 FE A 303 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 17 NE2 REMARK 620 2 HIS A 19 NE2 101.7 REMARK 620 3 GLU A 74 OE1 89.7 85.7 REMARK 620 4 ASP A 260 OD1 86.7 88.9 172.8 REMARK 620 5 PO4 A 304 O4 173.1 85.0 92.6 91.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 24 OD2 REMARK 620 2 HIS A 49 NE2 93.1 REMARK 620 3 HIS A 262 NE2 97.0 149.9 REMARK 620 4 PO4 A 304 O3 108.5 103.2 100.3 REMARK 620 5 PO4 A 304 O4 169.7 90.5 84.5 61.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 302 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 74 OE2 REMARK 620 2 HIS A 85 ND1 81.1 REMARK 620 3 HIS A 202 NE2 113.2 94.4 REMARK 620 4 PO4 A 304 O2 106.8 86.9 139.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 387987 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3E0F A 1 300 UNP A1A2L3 A1A2L3_BIFAA 1 300 SEQADV 3E0F GLY A 0 UNP A1A2L3 EXPRESSION TAG SEQRES 1 A 301 GLY MSE SER HIS VAL SER TYR ALA GLU PRO PRO ALA GLN SEQRES 2 A 301 GLY TRP ASP ILE HIS CYS HIS THR VAL PHE SER ASP GLY SEQRES 3 A 301 THR GLU THR PRO ARG THR LEU VAL GLU GLN ALA ARG LYS SEQRES 4 A 301 LEU GLY LEU HIS GLY VAL ALA ILE ALA ASP HIS ASP THR SEQRES 5 A 301 THR ALA GLY TRP ASP GLU ALA THR GLU ALA SER GLU GLU SEQRES 6 A 301 ILE GLY LEU PRO LEU LEU LEU GLY THR GLU ILE THR ALA SEQRES 7 A 301 VAL ASP GLU ASP VAL SER VAL HIS MSE LEU ALA PHE GLN SEQRES 8 A 301 TYR ASP PRO SER ASN GLU HIS ILE SER SER MSE PHE ALA SEQRES 9 A 301 ASN THR ARG ALA ALA ARG LEU ARG ARG THR LYS ARG MSE SEQRES 10 A 301 VAL GLU ARG LEU SER GLN ASP PHE PRO ILE THR TRP ASP SEQRES 11 A 301 ASP VAL LEU ALA GLN VAL LYS GLU GLY GLU ARG THR THR SEQRES 12 A 301 ILE GLY ARG PRO HIS ILE ALA ASP ALA LEU VAL ALA ALA SEQRES 13 A 301 GLY VAL TYR GLU THR ARG SER ASP ALA PHE ALA ASP ALA SEQRES 14 A 301 VAL SER ALA LYS SER LYS TYR TYR ILE PRO THR PRO SER SEQRES 15 A 301 PRO SER THR HIS GLU VAL ILE ALA ALA VAL LYS GLY ALA SEQRES 16 A 301 GLY GLY VAL VAL VAL ALA ALA HIS ALA GLY ASP PRO GLN SEQRES 17 A 301 ARG ASN ARG ARG LEU LEU SER ASP GLU GLN LEU ASP ALA SEQRES 18 A 301 MSE ILE ALA ASP GLY LEU ASP GLY LEU GLU VAL TRP HIS SEQRES 19 A 301 ARG GLY ASN PRO PRO GLU GLN ARG GLU ARG LEU LEU THR SEQRES 20 A 301 ILE ALA ALA ARG HIS ASP LEU LEU VAL THR GLY GLY SER SEQRES 21 A 301 ASP TRP HIS GLY LYS GLY LYS PRO ASN GLY LEU GLY GLU SEQRES 22 A 301 ASN LEU THR ASP ASP ASP THR VAL ARG GLU ILE LEU CYS SEQRES 23 A 301 ARG GLY VAL ASP LEU ILE GLY ARG VAL GLY SER SER HIS SEQRES 24 A 301 ALA ALA MODRES 3E0F MSE A 86 MET SELENOMETHIONINE MODRES 3E0F MSE A 101 MET SELENOMETHIONINE MODRES 3E0F MSE A 116 MET SELENOMETHIONINE MODRES 3E0F MSE A 221 MET SELENOMETHIONINE HET MSE A 86 8 HET MSE A 101 8 HET MSE A 116 8 HET MSE A 221 8 HET ZN A 301 1 HET FE A 302 1 HET FE A 303 1 HET PO4 A 304 5 HET PO4 A 305 5 HET ACT A 306 4 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM FE FE (III) ION HETNAM PO4 PHOSPHATE ION HETNAM ACT ACETATE ION FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 2 ZN ZN 2+ FORMUL 3 FE 2(FE 3+) FORMUL 5 PO4 2(O4 P 3-) FORMUL 7 ACT C2 H3 O2 1- FORMUL 8 HOH *103(H2 O) HELIX 1 1 THR A 28 LEU A 39 1 12 HELIX 2 2 GLY A 54 GLY A 66 1 13 HELIX 3 3 ASN A 95 SER A 121 1 27 HELIX 4 4 THR A 127 ALA A 133 1 7 HELIX 5 5 GLU A 137 THR A 141 5 5 HELIX 6 6 GLY A 144 ALA A 155 1 12 HELIX 7 7 THR A 160 ALA A 166 1 7 HELIX 8 8 SER A 183 ALA A 194 1 12 HELIX 9 9 SER A 214 GLY A 225 1 12 HELIX 10 10 PRO A 237 ASP A 252 1 16 HELIX 11 11 HIS A 262 LYS A 266 5 5 HELIX 12 12 ASP A 276 GLY A 287 1 12 SHEET 1 A 7 TRP A 14 CYS A 18 0 SHEET 2 A 7 GLY A 43 HIS A 49 1 O ALA A 47 N CYS A 18 SHEET 3 A 7 LEU A 69 ASP A 79 1 O LEU A 70 N VAL A 44 SHEET 4 A 7 VAL A 82 PHE A 89 -1 O MSE A 86 N ILE A 75 SHEET 5 A 7 VAL A 197 ALA A 201 -1 O ALA A 201 N HIS A 85 SHEET 6 A 7 GLY A 228 TRP A 232 1 O GLU A 230 N ALA A 200 SHEET 7 A 7 LEU A 254 GLY A 257 1 O LEU A 254 N LEU A 229 LINK C HIS A 85 N MSE A 86 1555 1555 1.33 LINK C MSE A 86 N LEU A 87 1555 1555 1.32 LINK C SER A 100 N MSE A 101 1555 1555 1.32 LINK C MSE A 101 N PHE A 102 1555 1555 1.33 LINK C ARG A 115 N MSE A 116 1555 1555 1.34 LINK C MSE A 116 N VAL A 117 1555 1555 1.33 LINK C ALA A 220 N MSE A 221 1555 1555 1.33 LINK C MSE A 221 N ILE A 222 1555 1555 1.34 LINK NE2 HIS A 17 FE FE A 303 1555 1555 2.21 LINK NE2 HIS A 19 FE FE A 303 1555 1555 2.30 LINK OD2 ASP A 24 ZN ZN A 301 1555 1555 2.15 LINK NE2 HIS A 49 ZN ZN A 301 1555 1555 2.14 LINK OE2 GLU A 74 FE FE A 302 1555 1555 2.04 LINK OE1 GLU A 74 FE FE A 303 1555 1555 2.09 LINK ND1 HIS A 85 FE FE A 302 1555 1555 2.16 LINK NE2 HIS A 202 FE FE A 302 1555 1555 2.45 LINK OD1 ASP A 260 FE FE A 303 1555 1555 2.37 LINK NE2 HIS A 262 ZN ZN A 301 1555 1555 2.32 LINK ZN ZN A 301 O3 PO4 A 304 1555 1555 2.28 LINK ZN ZN A 301 O4 PO4 A 304 1555 1555 2.65 LINK FE FE A 302 O2 PO4 A 304 1555 1555 2.01 LINK FE FE A 303 O4 PO4 A 304 1555 1555 2.04 SITE 1 AC1 3 ASP A 24 HIS A 49 HIS A 262 SITE 1 AC2 3 GLU A 74 HIS A 85 HIS A 202 SITE 1 AC3 4 HIS A 17 HIS A 19 GLU A 74 ASP A 260 SITE 1 AC4 9 HIS A 19 ASP A 24 HIS A 49 GLU A 74 SITE 2 AC4 9 HIS A 85 ASP A 260 HIS A 262 LYS A 266 SITE 3 AC4 9 HOH A 346 SITE 1 AC5 6 ARG A 109 ARG A 112 ARG A 145 HOH A 348 SITE 2 AC5 6 HOH A 367 HOH A 368 SITE 1 AC6 5 HIS A 185 ASP A 224 GLU A 239 HOH A 355 SITE 2 AC6 5 HOH A 363 CRYST1 102.460 102.460 54.170 90.00 90.00 120.00 P 65 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.009760 0.005635 0.000000 0.00000 SCALE2 0.000000 0.011270 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018460 0.00000