HEADER HYDROLASE 30-MAR-10 3MD7 TITLE CRYSTAL STRUCTURE OF A BETA-LACTAMASE-LIKE PROTEIN BOUND TO GMP FROM TITLE 2 BRUCELLA MELITENSIS 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: 3787676, BAB1_1016; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; 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, HYDROLASE, STRUCTURAL GENOMICS, SEATTLE KEYWDS 2 STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 4 03-APR-24 3MD7 1 REMARK REVDAT 3 21-FEB-24 3MD7 1 REMARK SEQADV LINK REVDAT 2 21-SEP-11 3MD7 1 JRNL VERSN REVDAT 1 21-APR-10 3MD7 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 BRABA.11339.A: ANOMALOUS DIFFRACTION AND LIGAND BINDING JRNL TITL 2 GUIDE TOWARDS THE ELUCIDATION OF THE FUNCTION OF A `PUTATIVE JRNL TITL 3 BETA-LACTAMASE-LIKE PROTEIN FROM BRUCELLA MELITENSIS. 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. 1.27 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) : 1.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.85 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 71085 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) : 0.108 REMARK 3 R VALUE (WORKING SET) : 0.107 REMARK 3 FREE R VALUE : 0.134 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3575 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) : 1.27 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.30 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4877 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.1520 REMARK 3 BIN FREE R VALUE SET COUNT : 222 REMARK 3 BIN FREE R VALUE : 0.2030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2116 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 341 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.14000 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): 0.034 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.034 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.019 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.939 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2336 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1600 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3209 ; 1.873 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3882 ; 1.044 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 305 ; 6.450 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;34.030 ;22.368 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 368 ;11.609 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.504 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 345 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2659 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 511 ; 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): 1404 ; 1.936 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 560 ; 0.629 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2297 ; 2.911 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 932 ; 3.945 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 895 ; 5.594 ; 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): 3936 ; 0.988 ; 1.000 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: HYDROGENS HAVE BEEN ADDED IN THE REMARK 4 REMARK 4 3MD7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058402. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.40 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9774 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71257 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.270 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.48900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: STRUCTURE SOLVED BY MOLECULAR REPLACEMENT USING REMARK 200 INITIAL MODEL FROM IODIDE SAD PHASING, CAN ALSO BE SOLVED USING REMARK 200 ANOMALOUS SIGNAL FROM MN AND K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MD PACT SCREEN, H9: 20% PEG 3350, REMARK 280 200MM K/NA TARTRATE, 100MM BISTRISPROPANE PH 8.6; BRABA.11339.A REMARK 280 AT 19.6MG/ML, PH 7.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 290K, PH 7.40 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 49.18000 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 49.18000 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 36.44500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.62500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.44500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.62500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.18000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.44500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 37.62500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.18000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.44500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 37.62500 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: 2920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 -49.18000 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 MET A -20 REMARK 465 ALA A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 MET A -12 REMARK 465 GLY A -11 REMARK 465 THR A -10 REMARK 465 LEU A -9 REMARK 465 GLU A -8 REMARK 465 ALA A -7 REMARK 465 GLN A -6 REMARK 465 THR A -5 REMARK 465 GLN A -4 REMARK 465 GLY A -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 THR A 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 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 GLU A 230 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 OD2 ASP A 172 O HOH A 333 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 320 O HOH A 321 4554 2.07 REMARK 500 O HOH A 292 O HOH A 563 4555 2.09 REMARK 500 O HOH A 292 O HOH A 575 4555 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 SER A 17 CB SER A 17 OG 0.138 REMARK 500 GLU A 254 CB GLU A 254 CG -0.128 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 40 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 MET A 69 CG - SD - CE ANGL. DEV. = 11.7 DEGREES REMARK 500 ARG A 179 NE - CZ - NH2 ANGL. DEV. = -4.1 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 ASP A 62 143.80 75.85 REMARK 500 PRO A 87 50.31 -98.98 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 NA A 306 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 56 O REMARK 620 2 ASN A 56 OD1 75.9 REMARK 620 3 HOH A 402 O 95.6 71.4 REMARK 620 4 HOH A 458 O 84.3 111.5 176.9 REMARK 620 5 HOH A 521 O 107.6 167.0 95.7 81.4 REMARK 620 N 1 2 3 4 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 87.4 REMARK 620 3 HIS A 170 NE2 94.1 94.8 REMARK 620 4 ASP A 188 OD2 87.5 173.2 90.0 REMARK 620 5 5GP A 303 O3P 178.3 91.1 86.7 93.9 REMARK 620 6 HOH A 330 O 102.8 99.6 158.2 77.2 76.7 REMARK 620 7 HOH A 340 O 171.0 92.4 76.9 93.4 9.8 86.1 REMARK 620 N 1 2 3 4 5 6 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 83.8 REMARK 620 3 ASP A 188 OD2 166.0 96.1 REMARK 620 4 HIS A 241 NE2 95.9 118.5 96.5 REMARK 620 5 5GP A 303 O1P 85.7 160.7 90.3 78.6 REMARK 620 6 HOH A 330 O 88.7 97.2 77.4 144.3 66.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 216 O REMARK 620 2 HOH A 375 O 72.3 REMARK 620 3 HOH A 396 O 98.8 160.7 REMARK 620 4 HOH A 416 O 148.1 88.7 106.1 REMARK 620 5 HOH A 496 O 117.4 79.9 89.6 82.9 REMARK 620 N 1 2 3 4 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 71.9 REMARK 620 3 THR A 255 O 78.7 70.7 REMARK 620 4 PRO A 256 O 143.8 94.9 65.1 REMARK 620 5 VAL A 259 O 135.4 76.6 119.2 68.4 REMARK 620 6 HOH A 431 O 117.8 151.3 135.8 90.2 79.1 REMARK 620 7 HOH A 599 O 80.3 135.3 69.9 87.4 142.9 73.1 REMARK 620 N 1 2 3 4 5 6 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 NA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 5GP A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 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: BRABA.11339.A RELATED DB: TARGETDB DBREF 3MD7 A 1 272 UNP Q2YQ74 Q2YQ74_BRUA2 1 272 SEQADV 3MD7 MET A -20 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 ALA A -19 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 HIS A -18 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 HIS A -17 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 HIS A -16 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 HIS A -15 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 HIS A -14 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 HIS A -13 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 MET A -12 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 GLY A -11 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 THR A -10 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 LEU A -9 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 GLU A -8 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 ALA A -7 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 GLN A -6 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 THR A -5 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 GLN A -4 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 GLY A -3 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 PRO A -2 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 GLY A -1 UNP Q2YQ74 EXPRESSION TAG SEQADV 3MD7 SER A 0 UNP Q2YQ74 EXPRESSION TAG SEQRES 1 A 293 MET ALA HIS HIS HIS HIS HIS HIS MET GLY THR LEU GLU SEQRES 2 A 293 ALA GLN THR GLN GLY PRO GLY SER MET THR SER PRO ARG SEQRES 3 A 293 ASN CYS LEU ARG PHE THR LEU LEU GLY CYS GLY SER SER SEQRES 4 A 293 PRO GLY VAL PRO ARG ILE ASN GLY ASP TRP GLY LYS CYS SEQRES 5 A 293 ASP PRO LYS ASN PRO LYS ASN ARG ARG ARG ARG ALA SER SEQRES 6 A 293 LEU LEU VAL GLU ARG TYR ASP ALA GLU GLY ASN ASN THR SEQRES 7 A 293 VAL VAL VAL ILE ASP THR GLY PRO ASP PHE ARG MET GLN SEQRES 8 A 293 MET ILE ASP SER GLY VAL HIS MET LEU ASP ALA ALA VAL SEQRES 9 A 293 TYR THR HIS PRO HIS ALA ASP HIS ILE HIS GLY ILE ASP SEQRES 10 A 293 ASP LEU ARG THR TYR VAL VAL ASP ASN GLY ARG LEU MET SEQRES 11 A 293 ASP VAL TYR ALA ASN ARG LEU THR ARG ASN ARG LEU TYR SEQRES 12 A 293 ASP THR PHE GLY TYR CYS PHE GLU THR PRO VAL GLY SER SEQRES 13 A 293 SER TYR PRO PRO ILE LEU SER MET HIS ASP ILE ALA PRO SEQRES 14 A 293 GLU THR PRO PHE SER ILE GLU GLY ALA GLY GLY ALA ILE SEQRES 15 A 293 ARG PHE GLU PRO PHE SER GLN VAL HIS GLY ASP ILE GLU SEQRES 16 A 293 SER LEU GLY PHE ARG ILE GLY SER VAL VAL TYR CYS THR SEQRES 17 A 293 ASP VAL SER ALA PHE PRO GLU GLN SER LEU GLN TYR ILE SEQRES 18 A 293 LYS ASP ALA ASP VAL LEU ILE ILE GLY ALA LEU GLN TYR SEQRES 19 A 293 ARG PRO HIS PRO SER HIS PHE SER LEU GLY GLU ALA LEU SEQRES 20 A 293 GLU TRP ILE GLU LYS LEU SER PRO LYS ARG ALA ILE LEU SEQRES 21 A 293 THR HIS MET HIS VAL PRO LEU ASP TYR GLU THR VAL MET SEQRES 22 A 293 ARG GLU THR PRO HIS HIS VAL GLU PRO GLY TYR ASP GLY SEQRES 23 A 293 LEU ARG PHE GLU VAL ALA VAL HET MN A 300 1 HET MN A 301 1 HET K A 302 1 HET NA A 305 1 HET NA A 306 1 HET 5GP A 303 24 HET TLA A 304 10 HETNAM MN MANGANESE (II) ION HETNAM K POTASSIUM ION HETNAM NA SODIUM ION HETNAM 5GP GUANOSINE-5'-MONOPHOSPHATE HETNAM TLA L(+)-TARTARIC ACID FORMUL 2 MN 2(MN 2+) FORMUL 4 K K 1+ FORMUL 5 NA 2(NA 1+) FORMUL 7 5GP C10 H14 N5 O8 P FORMUL 8 TLA C4 H6 O6 FORMUL 9 HOH *341(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 ARG A 267 VAL A 270 -1 O PHE A 268 N PHE A 10 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 O ASN A 56 NA NA A 306 1555 1555 2.44 LINK OD1 ASN A 56 NA NA A 306 1555 1555 2.64 LINK NE2 HIS A 86 MN MN A 301 1555 1555 2.24 LINK ND1 HIS A 88 MN MN A 301 1555 1555 2.22 LINK OD2 ASP A 90 MN MN A 300 1555 1555 2.28 LINK NE2 HIS A 91 MN MN A 300 1555 1555 2.25 LINK NE2 HIS A 170 MN MN A 301 1555 1555 2.22 LINK OD2 ASP A 188 MN MN A 300 1555 1555 2.28 LINK OD2 ASP A 188 MN MN A 301 1555 1555 2.32 LINK O HIS A 216 NA NA A 305 1555 1555 2.43 LINK NE2 HIS A 241 MN MN A 300 1555 1555 2.23 LINK O MET A 252 K K A 302 1555 1555 2.71 LINK OG1 THR A 255 K K A 302 1555 1555 2.74 LINK O THR A 255 K K A 302 1555 1555 2.88 LINK O PRO A 256 K K A 302 1555 1555 2.69 LINK O VAL A 259 K K A 302 1555 1555 2.61 LINK MN MN A 300 O1P 5GP A 303 1555 1555 2.38 LINK MN MN A 300 O HOH A 330 1555 1555 2.10 LINK MN MN A 301 O3P 5GP A 303 1555 1555 2.20 LINK MN MN A 301 O HOH A 330 1555 1555 2.07 LINK MN MN A 301 O HOH A 340 1555 1555 2.35 LINK K K A 302 O HOH A 431 1555 1555 3.49 LINK K K A 302 O HOH A 599 1555 1555 2.87 LINK NA NA A 305 O HOH A 375 1555 1555 2.67 LINK NA NA A 305 O HOH A 396 1555 1555 2.39 LINK NA NA A 305 O HOH A 416 1555 1555 2.45 LINK NA NA A 305 O HOH A 496 1555 1555 2.54 LINK NA NA A 306 O HOH A 402 1555 1555 2.53 LINK NA NA A 306 O HOH A 458 1555 1555 2.49 LINK NA NA A 306 O HOH A 521 1555 1555 2.43 CISPEP 1 VAL A 21 PRO A 22 0 -5.98 SITE 1 AC1 7 ASP A 90 HIS A 91 ASP A 188 HIS A 241 SITE 2 AC1 7 MN A 301 5GP A 303 HOH A 330 SITE 1 AC2 8 HIS A 86 HIS A 88 HIS A 170 ASP A 188 SITE 2 AC2 8 MN A 300 5GP A 303 HOH A 330 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 599 SITE 1 AC4 5 HIS A 216 HOH A 375 HOH A 396 HOH A 416 SITE 2 AC4 5 HOH A 496 SITE 1 AC5 5 ASN A 56 MET A 78 HOH A 402 HOH A 458 SITE 2 AC5 5 HOH A 521 SITE 1 AC6 24 SER A 18 PRO A 87 HIS A 88 ALA A 89 SITE 2 AC6 24 ASP A 90 HIS A 93 ASP A 96 ARG A 99 SITE 3 AC6 24 TYR A 127 TYR A 137 HIS A 170 ASP A 188 SITE 4 AC6 24 HIS A 219 HIS A 241 MN A 300 MN A 301 SITE 5 AC6 24 HOH A 315 HOH A 330 HOH A 340 HOH A 454 SITE 6 AC6 24 HOH A 502 HOH A 508 HOH A 511 HOH A 528 SITE 1 AC7 10 ARG A 23 LYS A 30 GLN A 212 HIS A 216 SITE 2 AC7 10 HIS A 243 HOH A 283 HOH A 341 HOH A 455 SITE 3 AC7 10 HOH A 460 HOH A 543 CRYST1 72.890 75.250 98.360 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 0.013719 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013289 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010167 0.00000