HEADER HYDROLASE 31-AUG-09 3IUU TITLE CRYSTAL STRUCTURE OF PUTATIVE METALLOPEPTIDASE (YP_676511.1) FROM TITLE 2 MESORHIZOBIUM SP. BNC1 AT 2.13 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE METALLOPEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MLRC-LIKE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MESORHIZOBIUM SP.; SOURCE 3 ORGANISM_TAXID: 266779; SOURCE 4 STRAIN: BNC1; SOURCE 5 GENE: MESO_3979, YP_676511.1; 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 YP_676511.1, PUTATIVE METALLOPEPTIDASE, STRUCTURAL GENOMICS, JOINT KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 PSI-2, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3IUU 1 REMARK SEQADV REVDAT 4 24-JUL-19 3IUU 1 REMARK LINK REVDAT 3 25-OCT-17 3IUU 1 REMARK REVDAT 2 13-JUL-11 3IUU 1 VERSN REVDAT 1 15-SEP-09 3IUU 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE METALLOPEPTIDASE (YP_676511.1) JRNL TITL 2 FROM MESORHIZOBIUM SP. BNC1 AT 2.13 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0053 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) : 2.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 36013 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1798 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) : 2.13 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2453 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 138 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3786 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 314 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 29.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.72000 REMARK 3 B22 (A**2) : 0.72000 REMARK 3 B33 (A**2) : -1.07000 REMARK 3 B12 (A**2) : 0.36000 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): 0.197 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.198 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3989 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2657 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5439 ; 1.499 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6446 ; 0.910 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 506 ; 6.461 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 180 ;35.235 ;23.167 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 612 ;13.512 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;15.304 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 611 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4458 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 830 ; 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): 2484 ; 0.711 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1000 ; 0.192 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4007 ; 1.286 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1505 ; 2.247 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1425 ; 3.439 ; 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 0 A 493 REMARK 3 ORIGIN FOR THE GROUP (A): 4.5634 23.6196 179.0097 REMARK 3 T TENSOR REMARK 3 T11: 0.0070 T22: 0.1136 REMARK 3 T33: 0.0331 T12: -0.0173 REMARK 3 T13: -0.0023 T23: -0.0135 REMARK 3 L TENSOR REMARK 3 L11: 0.9063 L22: 0.4421 REMARK 3 L33: 0.1491 L12: -0.2293 REMARK 3 L13: -0.0724 L23: -0.0155 REMARK 3 S TENSOR REMARK 3 S11: 0.0076 S12: 0.0495 S13: -0.1348 REMARK 3 S21: 0.0348 S22: 0.0002 S23: 0.0244 REMARK 3 S31: 0.0017 S32: -0.0070 S33: -0.0077 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: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. REMARK 3 4. SULFATE AND POLYETHYLENE GLYCOL FRAGMENTS MODELLED ARE REMARK 3 PRESENT IN CYRO/CRYSTALLIZATION CONDITIONS. 5. ZINC AND REMARK 3 IMIDAZOLE WERE TENTATIVELY MODELLED IN THE ACTIVE SITE. ZINC IS REMARK 3 MODELED BASED ON DENSITY AN COORDINATION GEOMETRY. THE FINAL REMARK 3 METAL ION ASSIGNMENT IS PENDING FOLLOW-UP STUDIES. IMIDAZOLE IS REMARK 3 ASSIGNED BASED ON DENSITY, INTERACTION ENVIRONMENT AND PRESENCE REMARK 3 IN THE PROTEIN BUFFER . REMARK 4 REMARK 4 3IUU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000054892. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.29 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) : 0.97883,0.91837 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 : 36013 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.130 REMARK 200 RESOLUTION RANGE LOW (A) : 46.829 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.16500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.01100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 55.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M COBALT CHLORIDE, 1.636 M REMARK 280 AMMONIUM SULFATE, 0.1 M MES PH 6.29, ADDITIVE: 0.001 M MANGANESE REMARK 280 CHLORIDE, NANODROP, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 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 REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 207.15333 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 103.57667 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 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 207.15333 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 103.57667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 207.15333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 103.57667 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 207.15333 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 103.57667 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: ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE REMARK 300 ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN REMARK 300 SOLUTION. 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 494 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 MSE A 93 CG SE CE REMARK 470 LYS A 326 CE NZ REMARK 470 HIS A 359 ND1 CD2 CE1 NE2 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 CYS A 490 CB CYS A 490 SG -0.101 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 219 NE - CZ - NH1 ANGL. DEV. = 3.0 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 64 -96.68 -107.69 REMARK 500 GLU A 76 123.18 -31.56 REMARK 500 SER A 252 37.21 -143.41 REMARK 500 ASP A 333 84.57 -166.22 REMARK 500 ASN A 346 -14.83 89.96 REMARK 500 ASP A 401 -129.15 45.00 REMARK 500 THR A 470 -73.76 -124.09 REMARK 500 ALA A 486 81.95 -150.04 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 ZN A 495 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 138 OD1 REMARK 620 2 ASP A 138 OD2 57.1 REMARK 620 3 HIS A 140 ND1 95.4 150.1 REMARK 620 4 HIS A 162 NE2 97.9 95.8 100.1 REMARK 620 5 IMD A 496 N3 140.7 92.9 104.6 111.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 495 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 496 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 497 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 498 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 499 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 510 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 378347 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 3IUU A 1 494 UNP Q11B79 Q11B79_MESSB 1 494 SEQADV 3IUU GLY A 0 UNP Q11B79 EXPRESSION TAG SEQRES 1 A 495 GLY MSE ALA GLN ARG SER ILE LEU VAL GLY GLN ILE TRP SEQRES 2 A 495 HIS GLU GLY HIS SER PHE ASN PRO ILE LEU THR ARG GLU SEQRES 3 A 495 LYS ASP PHE LEU PHE LEU ARG GLY GLU ALA VAL LEU GLU SEQRES 4 A 495 GLU ALA ARG ALA SER SER THR ALA LEU SER GLY ILE VAL SEQRES 5 A 495 LYS THR ALA GLU ALA LEU GLY TYR ARG CYS VAL PRO SER SEQRES 6 A 495 ILE SER ALA ARG ALA ARG PRO GLY GLY ALA ILE GLU GLN SEQRES 7 A 495 LYS VAL PHE ASP ASN ILE VAL ASP GLU PHE VAL GLN ALA SEQRES 8 A 495 ALA ARG MSE GLN ASP PHE ASP ALA ILE CYS LEU ASP LEU SEQRES 9 A 495 HIS GLY ALA THR LEU ALA GLU HIS THR LEU ASP THR GLU SEQRES 10 A 495 GLY TYR LEU LEU SER ARG LEU ARG GLU VAL VAL GLY ASN SEQRES 11 A 495 ASP ILE MSE ILE SER LEU ALA LEU ASP LEU HIS ALA TYR SEQRES 12 A 495 LEU THR PRO GLN MSE VAL GLU GLN ALA THR ILE ILE THR SEQRES 13 A 495 SER PHE ARG THR THR PRO HIS ALA ASP ILE GLU GLU THR SEQRES 14 A 495 GLY VAL ARG ALA MSE THR LEU LEU ASP SER LEU SER ASN SEQRES 15 A 495 GLU THR ARG PRO PRO ARG ALA ILE TYR SER LEU ILE PRO SEQRES 16 A 495 PHE LEU THR ARG GLY ASN ASP GLU THR TRP SER GLY PRO SEQRES 17 A 495 LEU ALA GLU ILE GLY ALA ALA ALA ASP ARG TRP ARG ALA SEQRES 18 A 495 ARG SER ASP VAL VAL ASP LEU SER ILE PHE ASN VAL HIS SEQRES 19 A 495 PRO PHE LEU ASP VAL PRO GLY TYR GLY GLN VAL VAL LEU SEQRES 20 A 495 ALA TYR ASP ASN GLY SER GLY ALA ALA ILE ASP ALA CYS SEQRES 21 A 495 ARG ASP LEU SER ASP MSE LEU TRP LYS ALA ARG ASP GLU SEQRES 22 A 495 PHE GLN GLU GLN LEU MSE SER VAL ASP LYS ALA LEU GLU SEQRES 23 A 495 ILE ALA ARG THR SER ARG GLN LEU LEU ALA LEU GLY ASP SEQRES 24 A 495 GLN GLY ASP ARG VAL MSE GLY ALA GLY PRO GLY ASP SER SEQRES 25 A 495 PRO GLU ILE ALA ARG VAL ALA LEU GLU HIS PHE PRO GLY SEQRES 26 A 495 LEU LYS VAL ALA VAL PRO VAL TYR ASP PRO GLN ALA VAL SEQRES 27 A 495 ARG THR ALA ARG GLU ALA GLY GLU ASN ALA THR VAL ARG SEQRES 28 A 495 MSE ALA VAL GLY GLY ALA PHE THR HIS SER VAL ALA PRO SEQRES 29 A 495 LEU GLU ARG ASP TRP THR VAL ARG LYS LEU CYS ARG ALA SEQRES 30 A 495 ARG PHE THR ASN ILE GLY PRO TYR MSE ALA GLY THR GLU SEQRES 31 A 495 ALA ASP PHE GLY ASP ALA ALA VAL LEU THR CYS ASP ALA SEQRES 32 A 495 VAL THR VAL ILE VAL THR THR MSE ALA PRO ASN VAL HIS SEQRES 33 A 495 ASP PRO ALA PHE TYR GLU ALA VAL GLY VAL PRO LEU ALA SEQRES 34 A 495 SER GLN GLN ALA VAL VAL ALA ARG ALA ALA ASN HIS TYR SEQRES 35 A 495 LYS LEU SER PHE ALA ASP ILE ALA ARG THR ILE THR VAL SEQRES 36 A 495 ASP THR PRO GLY LEU THR ALA PHE LYS PRO HIS GLN PHE SEQRES 37 A 495 PRO PHE THR GLN ALA ARG PRO PHE TYR PRO LEU ASP ILE SEQRES 38 A 495 VAL GLN TRP SER PHE ALA PRO LEU GLU CYS ASN LYS VAL SEQRES 39 A 495 GLY MODRES 3IUU MSE A 1 MET SELENOMETHIONINE MODRES 3IUU MSE A 93 MET SELENOMETHIONINE MODRES 3IUU MSE A 132 MET SELENOMETHIONINE MODRES 3IUU MSE A 147 MET SELENOMETHIONINE MODRES 3IUU MSE A 173 MET SELENOMETHIONINE MODRES 3IUU MSE A 265 MET SELENOMETHIONINE MODRES 3IUU MSE A 278 MET SELENOMETHIONINE MODRES 3IUU MSE A 304 MET SELENOMETHIONINE MODRES 3IUU MSE A 351 MET SELENOMETHIONINE MODRES 3IUU MSE A 385 MET SELENOMETHIONINE MODRES 3IUU MSE A 410 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 93 5 HET MSE A 132 8 HET MSE A 147 8 HET MSE A 173 8 HET MSE A 265 8 HET MSE A 278 8 HET MSE A 304 8 HET MSE A 351 8 HET MSE A 385 8 HET MSE A 410 8 HET ZN A 495 1 HET IMD A 496 5 HET SO4 A 497 5 HET SO4 A 498 5 HET SO4 A 499 5 HET SO4 A 500 5 HET SO4 A 501 5 HET SO4 A 502 5 HET SO4 A 503 5 HET SO4 A 504 5 HET SO4 A 505 5 HET SO4 A 506 5 HET SO4 A 507 5 HET PGE A 508 10 HET PGE A 509 10 HET PEG A 510 7 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM IMD IMIDAZOLE HETNAM SO4 SULFATE ION HETNAM PGE TRIETHYLENE GLYCOL HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 2 ZN ZN 2+ FORMUL 3 IMD C3 H5 N2 1+ FORMUL 4 SO4 11(O4 S 2-) FORMUL 15 PGE 2(C6 H14 O4) FORMUL 17 PEG C4 H10 O3 FORMUL 18 HOH *314(H2 O) HELIX 1 1 ARG A 24 LYS A 26 5 3 HELIX 2 2 GLY A 33 ALA A 42 1 10 HELIX 3 3 THR A 45 LEU A 57 1 13 HELIX 4 4 GLU A 76 GLN A 94 1 19 HELIX 5 5 ASP A 114 GLY A 128 1 15 HELIX 6 6 THR A 144 ALA A 151 1 8 HELIX 7 7 ASP A 164 LEU A 179 1 16 HELIX 8 8 GLY A 206 ALA A 220 1 15 HELIX 9 9 ALA A 254 ALA A 269 1 16 HELIX 10 10 ARG A 270 PHE A 273 5 4 HELIX 11 11 SER A 279 THR A 289 1 11 HELIX 12 12 GLY A 300 ALA A 306 5 7 HELIX 13 13 PRO A 312 PHE A 322 1 11 HELIX 14 14 ASP A 333 GLY A 344 1 12 HELIX 15 15 PRO A 417 VAL A 423 1 7 HELIX 16 16 PRO A 426 GLN A 430 5 5 HELIX 17 17 TYR A 441 ALA A 446 1 6 HELIX 18 18 LYS A 463 PHE A 467 5 5 SHEET 1 A 6 PHE A 28 ARG A 32 0 SHEET 2 A 6 ARG A 60 ALA A 69 -1 O ARG A 68 N LEU A 29 SHEET 3 A 6 SER A 5 TRP A 12 1 N ILE A 6 O ARG A 60 SHEET 4 A 6 ALA A 98 LEU A 103 1 O CYS A 100 N LEU A 7 SHEET 5 A 6 MSE A 132 LEU A 137 1 O ALA A 136 N LEU A 101 SHEET 6 A 6 ILE A 153 SER A 156 1 O THR A 155 N LEU A 137 SHEET 1 B 2 GLY A 15 HIS A 16 0 SHEET 2 B 2 GLY A 72 GLY A 73 1 O GLY A 72 N HIS A 16 SHEET 1 C 4 ASP A 226 PHE A 230 0 SHEET 2 C 4 GLN A 243 ASP A 249 -1 O VAL A 244 N PHE A 230 SHEET 3 C 4 ARG A 187 ILE A 193 -1 N ILE A 193 O GLN A 243 SHEET 4 C 4 LEU A 488 CYS A 490 -1 O CYS A 490 N ALA A 188 SHEET 1 D 8 THR A 348 VAL A 353 0 SHEET 2 D 8 LEU A 364 THR A 379 -1 O LEU A 364 N VAL A 353 SHEET 3 D 8 GLU A 389 CYS A 400 -1 O GLY A 393 N ALA A 376 SHEET 4 D 8 VAL A 403 THR A 408 -1 O VAL A 405 N LEU A 398 SHEET 5 D 8 VAL A 327 TYR A 332 1 N VAL A 331 O ILE A 406 SHEET 6 D 8 ALA A 432 ALA A 435 1 O ALA A 432 N ALA A 328 SHEET 7 D 8 LEU A 293 ASP A 298 1 N LEU A 296 O VAL A 433 SHEET 8 D 8 ALA A 449 VAL A 454 1 O ARG A 450 N ALA A 295 LINK C GLY A 0 N MSE A 1 1555 1555 1.32 LINK C MSE A 1 N ALA A 2 1555 1555 1.33 LINK C ARG A 92 N MSE A 93 1555 1555 1.34 LINK C MSE A 93 N GLN A 94 1555 1555 1.34 LINK C ILE A 131 N MSE A 132 1555 1555 1.31 LINK C MSE A 132 N ILE A 133 1555 1555 1.32 LINK C GLN A 146 N MSE A 147 1555 1555 1.34 LINK C MSE A 147 N VAL A 148 1555 1555 1.32 LINK C ALA A 172 N MSE A 173 1555 1555 1.32 LINK C MSE A 173 N THR A 174 1555 1555 1.33 LINK C ASP A 264 N MSE A 265 1555 1555 1.34 LINK C MSE A 265 N LEU A 266 1555 1555 1.33 LINK C LEU A 277 N MSE A 278 1555 1555 1.33 LINK C MSE A 278 N SER A 279 1555 1555 1.32 LINK C VAL A 303 N MSE A 304 1555 1555 1.33 LINK C MSE A 304 N GLY A 305 1555 1555 1.35 LINK C ARG A 350 N MSE A 351 1555 1555 1.33 LINK C MSE A 351 N ALA A 352 1555 1555 1.33 LINK C TYR A 384 N MSE A 385 1555 1555 1.33 LINK C MSE A 385 N ALA A 386 1555 1555 1.33 LINK C THR A 409 N MSE A 410 1555 1555 1.34 LINK C MSE A 410 N ALA A 411 1555 1555 1.34 LINK OD1 ASP A 138 ZN ZN A 495 1555 1555 2.18 LINK OD2 ASP A 138 ZN ZN A 495 1555 1555 2.40 LINK ND1 HIS A 140 ZN ZN A 495 1555 1555 2.08 LINK NE2 HIS A 162 ZN ZN A 495 1555 1555 2.11 LINK ZN ZN A 495 N3 IMD A 496 1555 1555 2.14 CISPEP 1 THR A 160 PRO A 161 0 -2.59 CISPEP 2 GLY A 382 PRO A 383 0 9.32 CISPEP 3 ARG A 473 PRO A 474 0 0.43 CISPEP 4 TYR A 476 PRO A 477 0 16.46 SITE 1 AC1 4 ASP A 138 HIS A 140 HIS A 162 IMD A 496 SITE 1 AC2 7 GLU A 14 HIS A 104 ASP A 138 HIS A 140 SITE 2 AC2 7 HIS A 162 MSE A 304 ZN A 495 SITE 1 AC3 9 ARG A 302 MSE A 304 ALA A 437 ALA A 438 SITE 2 AC3 9 ASN A 439 HIS A 440 HOH A 616 HOH A 651 SITE 3 AC3 9 HOH A 718 SITE 1 AC4 4 LYS A 26 ARG A 375 HOH A 743 HOH A 749 SITE 1 AC5 3 ARG A 24 ARG A 338 HOH A 692 SITE 1 AC6 2 ARG A 316 HIS A 321 SITE 1 AC7 3 ARG A 187 GLY A 253 ILE A 256 SITE 1 AC8 3 LYS A 463 ARG A 473 HOH A 783 SITE 1 AC9 2 GLU A 34 HOH A 773 SITE 1 BC1 1 ARG A 288 SITE 1 BC2 1 ARG A 341 SITE 1 BC3 1 ARG A 221 SITE 1 BC4 2 CYS A 374 ARG A 375 SITE 1 BC5 6 GLU A 182 ARG A 184 PRO A 185 PRO A 186 SITE 2 BC5 6 VAL A 225 ASN A 250 SITE 1 BC6 4 ARG A 260 PHE A 485 PRO A 487 HOH A 577 SITE 1 BC7 6 LYS A 26 ARG A 377 ASP A 391 MSE A 410 SITE 2 BC7 6 HOH A 693 HOH A 716 CRYST1 82.220 82.220 310.730 90.00 90.00 120.00 P 62 2 2 12 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 0.012162 0.007022 0.000000 0.00000 SCALE2 0.000000 0.014044 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003218 0.00000