HEADER HYDROLASE 25-JAN-11 3QH8 TITLE CRYSTAL STRUCTURE OF A BETA-LACTAMASE-LIKE PROTEIN BOUND TO AMP FROM TITLE 2 BRUCELLA MELITENSIS, LONG WAVELENGTH SYNCHROTRON DATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTAMASE-LIKE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRUCELLA MELITENSIS BIOVAR ABORTUS; SOURCE 3 ORGANISM_TAXID: 359391; SOURCE 4 STRAIN: 2308; SOURCE 5 GENE: BAB1_1016; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: AVA0421 KEYWDS SSGCID, BETA-LACTAMASE LIKE, BRUCELLA MELITENSIS, AMP, MN CENTRE, KEYWDS 2 STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR KEYWDS 3 INFECTIOUS DISEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 4 13-SEP-23 3QH8 1 REMARK SEQADV LINK REVDAT 3 21-SEP-11 3QH8 1 JRNL REVDAT 2 13-JUL-11 3QH8 1 VERSN REVDAT 1 09-FEB-11 3QH8 0 JRNL AUTH J.ABENDROTH,B.SANKARAN,T.E.EDWARDS,A.S.GARDBERG,S.DIETERICH, JRNL AUTH 2 J.BHANDARI,A.J.NAPULI,W.C.VAN VOORHIS,B.L.STAKER,P.J.MYLER, JRNL AUTH 3 L.J.STEWART JRNL TITL CRYSTAL STRUCTURE OF A BETA-LACTAMASE-LIKE PROTEIN BOUND TO JRNL TITL 2 AMP FROM BRUCELLA MELITENSIS, LONG WAVELENGTH SYNCHROTRON JRNL TITL 3 DATA JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 67 1106 2011 JRNL REFN ESSN 1744-3091 JRNL PMID 21904058 JRNL DOI 10.1107/S1744309111010220 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 36263 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1868 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2400 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 144 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2118 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 314 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -0.20000 REMARK 3 B33 (A**2) : 0.39000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.074 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.587 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2289 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1560 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3133 ; 1.652 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3776 ; 0.983 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 293 ; 6.181 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 107 ;33.757 ;22.150 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 351 ;10.998 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;16.300 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 339 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2592 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 500 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1393 ; 0.937 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 557 ; 0.286 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2266 ; 1.657 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 896 ; 2.549 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 857 ; 4.038 ; 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 : 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 1 A 618 REMARK 3 ORIGIN FOR THE GROUP (A): 15.3140 -6.0390 -24.8600 REMARK 3 T TENSOR REMARK 3 T11: 0.0143 T22: 0.0186 REMARK 3 T33: 0.0043 T12: -0.0034 REMARK 3 T13: -0.0014 T23: 0.0048 REMARK 3 L TENSOR REMARK 3 L11: 0.3111 L22: 0.4369 REMARK 3 L33: 0.3116 L12: 0.0401 REMARK 3 L13: -0.0454 L23: 0.0997 REMARK 3 S TENSOR REMARK 3 S11: 0.0188 S12: 0.0042 S13: 0.0010 REMARK 3 S21: 0.0166 S22: -0.0253 S23: -0.0322 REMARK 3 S31: -0.0024 S32: 0.0256 S33: 0.0065 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 REMARK 4 REMARK 4 3QH8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063641. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.3476 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36362 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.0800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MR REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3MD7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-18% PEG 3350, 200MM K/NA TARTRATE, REMARK 280 100MM BISTRISPROPANE PH 8.0, BRABA.11339.A.PW27637 AT 18MG/ML REMARK 280 SUPPLEMENTED WITH 1MM AMPPNP AND 2MM MGCL2 AT 18MG/ML. CRYO: 21% REMARK 280 PEG 3350, 15% EG, 165MM K/NA TARTRATE, 87MM BISTRISPROPANE PH REMARK 280 8.0, 1MM AMPPNP, 2MM MGCL2, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 49.47000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.47000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 36.60500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.76500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.60500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.76500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.47000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.60500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.76500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.47000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.60500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.76500 REMARK 290 SMTRY3 8 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -46.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -49.47000 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 -1 REMARK 465 SER A 0 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 MET A 1 CG SD CE REMARK 470 THR A 2 OG1 CG2 REMARK 470 LYS A 34 CG CD CE NZ REMARK 470 ARG A 120 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 194 CG CD OE1 OE2 REMARK 470 LYS A 201 CG CD CE NZ REMARK 470 GLU A 230 CG CD OE1 OE2 REMARK 470 GLU A 249 CG CD OE1 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 NH2 ARG A 115 O HOH A 576 2.03 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 99 NE - CZ - NH1 ANGL. DEV. = -3.4 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 ASP A 62 141.05 73.74 REMARK 500 PRO A 87 57.76 -98.14 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 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 86 NE2 REMARK 620 2 HIS A 88 ND1 88.9 REMARK 620 3 HIS A 170 NE2 94.4 95.7 REMARK 620 4 ASP A 188 OD2 87.3 173.9 89.4 REMARK 620 5 AMP A 303 O1P 176.1 90.8 81.8 93.3 REMARK 620 6 HOH A 340 O 100.8 100.9 157.6 75.1 83.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 300 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 90 OD2 REMARK 620 2 HIS A 91 NE2 83.0 REMARK 620 3 ASP A 188 OD2 168.0 94.7 REMARK 620 4 HIS A 241 NE2 96.0 115.5 95.6 REMARK 620 5 AMP A 303 O3P 89.5 161.9 89.2 81.5 REMARK 620 6 HOH A 340 O 89.4 94.2 79.0 150.2 69.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 302 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 252 O REMARK 620 2 THR A 255 OG1 70.3 REMARK 620 3 THR A 255 O 76.8 69.4 REMARK 620 4 PRO A 256 O 141.6 94.6 64.8 REMARK 620 5 VAL A 259 O 136.1 77.7 118.9 68.5 REMARK 620 6 HOH A 545 O 81.1 131.7 66.7 84.2 142.4 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 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TLA A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3MD7 RELATED DB: PDB REMARK 900 NATIVE REMARK 900 RELATED ID: 3PY5 RELATED DB: PDB REMARK 900 AMP, IN HOUSE REMARK 900 RELATED ID: 3PY6 RELATED DB: PDB REMARK 900 GMP, IN HOUSE REMARK 900 RELATED ID: BRABA.11339.A RELATED DB: TARGETDB DBREF 3QH8 A 1 272 UNP Q2YQ74 Q2YQ74_BRUA2 1 272 SEQADV 3QH8 GLY A -1 UNP Q2YQ74 EXPRESSION TAG SEQADV 3QH8 SER A 0 UNP Q2YQ74 EXPRESSION TAG SEQRES 1 A 274 GLY SER MET THR SER PRO ARG ASN CYS LEU ARG PHE THR SEQRES 2 A 274 LEU LEU GLY CYS GLY SER SER PRO GLY VAL PRO ARG ILE SEQRES 3 A 274 ASN GLY ASP TRP GLY LYS CYS ASP PRO LYS ASN PRO LYS SEQRES 4 A 274 ASN ARG ARG ARG ARG ALA SER LEU LEU VAL GLU ARG TYR SEQRES 5 A 274 ASP ALA GLU GLY ASN ASN THR VAL VAL VAL ILE ASP THR SEQRES 6 A 274 GLY PRO ASP PHE ARG MET GLN MET ILE ASP SER GLY VAL SEQRES 7 A 274 HIS MET LEU ASP ALA ALA VAL TYR THR HIS PRO HIS ALA SEQRES 8 A 274 ASP HIS ILE HIS GLY ILE ASP ASP LEU ARG THR TYR VAL SEQRES 9 A 274 VAL ASP ASN GLY ARG LEU MET ASP VAL TYR ALA ASN ARG SEQRES 10 A 274 LEU THR ARG ASN ARG LEU TYR ASP THR PHE GLY TYR CYS SEQRES 11 A 274 PHE GLU THR PRO VAL GLY SER SER TYR PRO PRO ILE LEU SEQRES 12 A 274 SER MET HIS ASP ILE ALA PRO GLU THR PRO PHE SER ILE SEQRES 13 A 274 GLU GLY ALA GLY GLY ALA ILE ARG PHE GLU PRO PHE SER SEQRES 14 A 274 GLN VAL HIS GLY ASP ILE GLU SER LEU GLY PHE ARG ILE SEQRES 15 A 274 GLY SER VAL VAL TYR CYS THR ASP VAL SER ALA PHE PRO SEQRES 16 A 274 GLU GLN SER LEU GLN TYR ILE LYS ASP ALA ASP VAL LEU SEQRES 17 A 274 ILE ILE GLY ALA LEU GLN TYR ARG PRO HIS PRO SER HIS SEQRES 18 A 274 PHE SER LEU GLY GLU ALA LEU GLU TRP ILE GLU LYS LEU SEQRES 19 A 274 SER PRO LYS ARG ALA ILE LEU THR HIS MET HIS VAL PRO SEQRES 20 A 274 LEU ASP TYR GLU THR VAL MET ARG GLU THR PRO HIS HIS SEQRES 21 A 274 VAL GLU PRO GLY TYR ASP GLY LEU ARG PHE GLU VAL ALA SEQRES 22 A 274 VAL HET MN A 300 1 HET MN A 301 1 HET K A 302 1 HET AMP A 303 23 HET EDO A 305 4 HET TLA A 304 10 HETNAM MN MANGANESE (II) ION HETNAM K POTASSIUM ION HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM TLA L(+)-TARTARIC ACID HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MN 2(MN 2+) FORMUL 4 K K 1+ FORMUL 5 AMP C10 H14 N5 O7 P FORMUL 6 EDO C2 H6 O2 FORMUL 7 TLA C4 H6 O6 FORMUL 8 HOH *314(H2 O) HELIX 1 1 ASN A 35 ARG A 39 5 5 HELIX 2 2 ASP A 66 GLY A 75 1 10 HELIX 3 3 HIS A 88 HIS A 93 1 6 HELIX 4 4 GLY A 94 ASP A 97 5 4 HELIX 5 5 LEU A 98 GLY A 106 1 9 HELIX 6 6 ASN A 114 PHE A 125 1 12 HELIX 7 7 GLY A 126 PHE A 129 5 4 HELIX 8 8 PRO A 193 GLN A 195 5 3 HELIX 9 9 SER A 196 LYS A 201 1 6 HELIX 10 10 SER A 221 SER A 233 1 13 HELIX 11 11 ASP A 247 THR A 255 1 9 SHEET 1 A 7 LEU A 141 ASP A 145 0 SHEET 2 A 7 MET A 109 ALA A 113 1 N MET A 109 O SER A 142 SHEET 3 A 7 ALA A 81 VAL A 83 1 N ALA A 82 O TYR A 112 SHEET 4 A 7 ASN A 56 ILE A 61 1 N VAL A 60 O VAL A 83 SHEET 5 A 7 SER A 44 TYR A 50 -1 N VAL A 47 O VAL A 59 SHEET 6 A 7 CYS A 7 GLY A 14 -1 N CYS A 7 O TYR A 50 SHEET 7 A 7 LEU A 266 VAL A 270 -1 O LEU A 266 N LEU A 12 SHEET 1 B 7 PHE A 152 ILE A 154 0 SHEET 2 B 7 ILE A 161 HIS A 170 -1 O PHE A 163 N PHE A 152 SHEET 3 B 7 ILE A 173 ILE A 180 -1 O ILE A 173 N HIS A 170 SHEET 4 B 7 VAL A 183 CYS A 186 -1 O VAL A 183 N ILE A 180 SHEET 5 B 7 VAL A 205 GLY A 209 1 O ILE A 207 N VAL A 184 SHEET 6 B 7 ARG A 236 THR A 240 1 O ILE A 238 N LEU A 206 SHEET 7 B 7 VAL A 259 PRO A 261 1 O GLU A 260 N LEU A 239 LINK NE2 HIS A 86 MN MN A 301 1555 1555 2.22 LINK ND1 HIS A 88 MN MN A 301 1555 1555 2.24 LINK OD2 ASP A 90 MN MN A 300 1555 1555 2.26 LINK NE2 HIS A 91 MN MN A 300 1555 1555 2.27 LINK NE2 HIS A 170 MN MN A 301 1555 1555 2.24 LINK OD2 ASP A 188 MN MN A 300 1555 1555 2.26 LINK OD2 ASP A 188 MN MN A 301 1555 1555 2.45 LINK NE2 HIS A 241 MN MN A 300 1555 1555 2.22 LINK O MET A 252 K K A 302 1555 1555 2.74 LINK OG1 THR A 255 K K A 302 1555 1555 2.76 LINK O THR A 255 K K A 302 1555 1555 2.96 LINK O PRO A 256 K K A 302 1555 1555 2.72 LINK O VAL A 259 K K A 302 1555 1555 2.64 LINK MN MN A 300 O3P AMP A 303 1555 1555 2.37 LINK MN MN A 300 O HOH A 340 1555 1555 2.07 LINK MN MN A 301 O1P AMP A 303 1555 1555 2.23 LINK MN MN A 301 O HOH A 340 1555 1555 2.05 LINK K K A 302 O HOH A 545 1555 1555 2.95 CISPEP 1 VAL A 21 PRO A 22 0 -4.79 SITE 1 AC1 7 ASP A 90 HIS A 91 ASP A 188 HIS A 241 SITE 2 AC1 7 MN A 301 AMP A 303 HOH A 340 SITE 1 AC2 7 HIS A 86 HIS A 88 HIS A 170 ASP A 188 SITE 2 AC2 7 MN A 300 AMP A 303 HOH A 340 SITE 1 AC3 5 MET A 252 THR A 255 PRO A 256 VAL A 259 SITE 2 AC3 5 HOH A 545 SITE 1 AC4 24 SER A 18 PRO A 87 HIS A 88 ALA A 89 SITE 2 AC4 24 ASP A 90 ASP A 96 ARG A 99 TYR A 127 SITE 3 AC4 24 TYR A 137 HIS A 170 ASP A 188 HIS A 219 SITE 4 AC4 24 HIS A 241 MN A 300 MN A 301 EDO A 305 SITE 5 AC4 24 HOH A 307 HOH A 340 HOH A 344 HOH A 426 SITE 6 AC4 24 HOH A 433 HOH A 484 HOH A 516 HOH A 588 SITE 1 AC5 5 HIS A 88 SER A 135 ASP A 172 AMP A 303 SITE 2 AC5 5 HOH A 332 SITE 1 AC6 9 ARG A 23 LYS A 30 GLN A 212 HIS A 216 SITE 2 AC6 9 HIS A 243 HOH A 338 HOH A 476 HOH A 598 SITE 3 AC6 9 HOH A 599 CRYST1 73.210 75.530 98.940 90.00 90.00 90.00 C 2 2 21 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 0.013659 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010107 0.00000