HEADER METAL BINDING PROTEIN 07-SEP-10 3ORU TITLE CRYSTAL STRUCTURE OF A DUF1989 FAMILY PROTEIN (TM1040_0329) FROM TITLE 2 SILICIBACTER SP. TM1040 AT 1.11 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUF1989 FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RUEGERIA SP. TM1040; SOURCE 3 ORGANISM_TAXID: 292414; SOURCE 4 GENE: TM1040_0329; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-BIOLOGY, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 06-NOV-24 3ORU 1 REMARK REVDAT 4 01-FEB-23 3ORU 1 REMARK SEQADV LINK REVDAT 3 25-OCT-17 3ORU 1 REMARK REVDAT 2 20-JUL-11 3ORU 1 KEYWDS REVDAT 1 13-OCT-10 3ORU 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A DUF1989 FAMILY PROTEIN (TM1040_0329) JRNL TITL 2 FROM SILICIBACTER SP. TM1040 AT 1.11 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.11 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 1.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 92207 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) : 0.127 REMARK 3 R VALUE (WORKING SET) : 0.126 REMARK 3 FREE R VALUE : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4612 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) : 1.11 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.14 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6229 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.1990 REMARK 3 BIN FREE R VALUE SET COUNT : 320 REMARK 3 BIN FREE R VALUE : 0.2310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1770 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 7.56 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.03000 REMARK 3 B22 (A**2) : 0.46000 REMARK 3 B33 (A**2) : -0.43000 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): 0.027 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.016 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.751 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.977 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1957 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 1387 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2696 ; 1.780 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3364 ; 0.992 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 267 ; 7.125 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 95 ;28.424 ;22.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 320 ;12.193 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;18.276 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 296 ; 0.108 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2259 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 414 ; 0.002 ; 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): 1223 ; 1.758 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 481 ; 0.757 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2001 ; 2.494 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 734 ; 3.099 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 677 ; 4.253 ; 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): 3344 ; 1.437 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 360 ; 9.738 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3280 ; 3.757 ; 3.000 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: 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. A ZINC ION (ZN) WAS MODELED BASED ON ELECTRON REMARK 3 DENSITY, ANOMALOUS DIFFERENCE FOURIER MAP, ZINC EMISSION LINES REMARK 3 IN X-RAY FLUORESCENCE SPECTRA AND COORDINATION GEOMETRY WITH REMARK 3 CYSTEINE RESIDUES. 4. MAGNESIUM ION (MG), WHICH WAS USED IN REMARK 3 CRYSTALLIZATION CONDITION (0.1 M), WAS MODELED BASED ON ELECTRON REMARK 3 DENSITY AND COORDINATION GEOMETRY. REMARK 4 REMARK 4 3ORU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-SEP-10. REMARK 100 THE DEPOSITION ID IS D_1000061493. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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) : 0.91837,0.97981,0.97944 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 : 92236 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.110 REMARK 200 RESOLUTION RANGE LOW (A) : 28.951 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.760 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.0900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.11 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 (%): 44.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22.0% PEG 3350, 0.10M MG CL, NANODROP, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 28.95100 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 28.95100 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 30.87850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.51200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.87850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.51200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 28.95100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.87850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.51200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 28.95100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.87850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.51200 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 300 REMARK: CRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE EXCLUSION REMARK 300 CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A REMARK 300 SIGNIFICATION OLIGOMERIZATION STATE IN 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -114.0 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 28.95100 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 ALA A 233 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 SER A 3 OG REMARK 470 ARG A 6 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 16 CD OE1 OE2 REMARK 470 GLU A 137 CG CD OE1 OE2 REMARK 470 ARG A 157 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 175 CD OE1 OE2 REMARK 470 ARG A 231 CZ NH1 NH2 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 NH2 ARG A 227 O HOH A 483 8545 2.18 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 29 NE - CZ - NH1 ANGL. DEV. = -4.9 DEGREES REMARK 500 ARG A 29 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 90 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 90 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 104 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 ASP A 210 15.18 -142.86 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 250 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 126 SG REMARK 620 2 CYS A 143 SG 110.4 REMARK 620 3 CYS A 207 SG 116.3 113.4 REMARK 620 4 HOH A 308 O 102.3 101.2 111.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 300 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 302 O REMARK 620 2 HOH A 303 O 87.6 REMARK 620 3 HOH A 304 O 80.0 85.0 REMARK 620 4 HOH A 305 O 94.9 177.5 95.9 REMARK 620 5 HOH A 306 O 165.7 83.2 88.2 94.5 REMARK 620 6 HOH A 307 O 95.4 85.0 169.2 94.3 94.7 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 ZN A 250 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 383406 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS 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 3ORU A 1 233 UNP Q1GJV4 Q1GJV4_SILST 1 233 SEQADV 3ORU GLY A 0 UNP Q1GJV4 EXPRESSION TAG SEQRES 1 A 234 GLY MSE THR SER PHE ASP ARG PRO PHE GLU ALA ALA ARG SEQRES 2 A 234 PRO ASP GLY GLU ASN PRO SER ALA HIS GLU THR LEU ALA SEQRES 3 A 234 GLU GLY GLY ARG LEU ARG PRO GLU ALA THR TYR THR ILE SEQRES 4 A 234 PRO ALA ARG GLN GLY ARG ALA ILE ARG MSE ALA GLN GLY SEQRES 5 A 234 GLU ALA LEU MSE VAL ILE ASN ARG ASP GLY SER GLN ILE SEQRES 6 A 234 GLY ASP PHE TRP ALA PHE VAL GLU GLY ASP CYS GLY GLU SEQRES 7 A 234 TYR LEU SER MSE GLU HIS LEU ARG PRO THR LEU ARG ARG SEQRES 8 A 234 VAL SER PRO ARG PRO GLY ASP VAL LEU VAL SER ASN ARG SEQRES 9 A 234 ARG ARG PRO ILE LEU THR LEU LEU GLU ASP SER SER PRO SEQRES 10 A 234 GLY VAL HIS ASP THR LEU VAL ALA SER CYS ASP VAL HIS SEQRES 11 A 234 ARG TYR ALA GLN LEU GLY HIS GLU GLY TYR HIS ASP ASN SEQRES 12 A 234 CYS THR ASP ASN LEU ARG MSE ALA LEU GLY ALA LEU GLY SEQRES 13 A 234 LEU ARG PRO THR THR VAL PRO CYS PRO LEU ASN LEU TRP SEQRES 14 A 234 MSE ASN THR PRO VAL VAL GLU GLY GLY ALA MSE GLU TRP SEQRES 15 A 234 ARG PRO PRO VAL SER ARG ARG GLY ASP HIS VAL LEU PHE SEQRES 16 A 234 ARG ALA GLU LEU ASP VAL VAL VAL VAL ILE SER CYS CYS SEQRES 17 A 234 PRO MSE ASP LEU LEU PRO ILE ASN GLY GLU GLU ALA GLN SEQRES 18 A 234 PRO ARG ALA LEU ASP VAL ARG LEU ARG PRO ARG PRO ALA MODRES 3ORU MSE A 48 MET SELENOMETHIONINE MODRES 3ORU MSE A 55 MET SELENOMETHIONINE MODRES 3ORU MSE A 81 MET SELENOMETHIONINE MODRES 3ORU MSE A 149 MET SELENOMETHIONINE MODRES 3ORU MSE A 169 MET SELENOMETHIONINE MODRES 3ORU MSE A 179 MET SELENOMETHIONINE MODRES 3ORU MSE A 209 MET SELENOMETHIONINE HET MSE A 48 8 HET MSE A 55 13 HET MSE A 81 8 HET MSE A 149 8 HET MSE A 169 13 HET MSE A 179 8 HET MSE A 209 8 HET ZN A 250 1 HET MG A 300 1 HET CL A 301 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION FORMUL 1 MSE 7(C5 H11 N O2 SE) FORMUL 2 ZN ZN 2+ FORMUL 3 MG MG 2+ FORMUL 4 CL CL 1- FORMUL 5 HOH *340(H2 O) HELIX 1 1 ASN A 17 HIS A 21 5 5 HELIX 2 2 ALA A 25 ARG A 29 5 5 HELIX 3 3 SER A 80 ARG A 89 1 10 HELIX 4 4 ASP A 127 LEU A 134 1 8 HELIX 5 5 ASN A 142 ALA A 153 1 12 SHEET 1 A 6 TYR A 36 ILE A 38 0 SHEET 2 A 6 LEU A 224 ARG A 229 -1 O LEU A 224 N ILE A 38 SHEET 3 A 6 ALA A 53 ILE A 57 -1 N ILE A 57 O ASP A 225 SHEET 4 A 6 HIS A 191 ALA A 196 -1 O PHE A 194 N LEU A 54 SHEET 5 A 6 PRO A 106 ASP A 113 -1 N LEU A 111 O LEU A 193 SHEET 6 A 6 VAL A 98 VAL A 100 -1 N LEU A 99 O LEU A 108 SHEET 1 B 4 GLY A 43 MSE A 48 0 SHEET 2 B 4 VAL A 200 CYS A 206 -1 O VAL A 202 N ILE A 46 SHEET 3 B 4 GLY A 65 VAL A 71 -1 N ASP A 66 O SER A 205 SHEET 4 B 4 ASP A 74 TYR A 78 -1 O ASP A 74 N VAL A 71 SHEET 1 C 4 GLY A 43 MSE A 48 0 SHEET 2 C 4 VAL A 200 CYS A 206 -1 O VAL A 202 N ILE A 46 SHEET 3 C 4 GLY A 65 VAL A 71 -1 N ASP A 66 O SER A 205 SHEET 4 C 4 LEU A 165 LEU A 167 -1 O LEU A 167 N GLY A 65 LINK C ARG A 47 N MSE A 48 1555 1555 1.32 LINK C MSE A 48 N ALA A 49 1555 1555 1.32 LINK C LEU A 54 N MSE A 55 1555 1555 1.33 LINK C MSE A 55 N VAL A 56 1555 1555 1.33 LINK C SER A 80 N MSE A 81 1555 1555 1.33 LINK C MSE A 81 N GLU A 82 1555 1555 1.34 LINK C ARG A 148 N MSE A 149 1555 1555 1.33 LINK C MSE A 149 N ALA A 150 1555 1555 1.34 LINK C TRP A 168 N MSE A 169 1555 1555 1.33 LINK C MSE A 169 N ASN A 170 1555 1555 1.33 LINK C ALA A 178 N MSE A 179 1555 1555 1.33 LINK C MSE A 179 N GLU A 180 1555 1555 1.32 LINK C PRO A 208 N MSE A 209 1555 1555 1.33 LINK C MSE A 209 N ASP A 210 1555 1555 1.32 LINK SG CYS A 126 ZN ZN A 250 1555 1555 2.35 LINK SG CYS A 143 ZN ZN A 250 1555 1555 2.32 LINK SG CYS A 207 ZN ZN A 250 1555 1555 2.30 LINK ZN ZN A 250 O HOH A 308 1555 1555 2.05 LINK MG MG A 300 O HOH A 302 1555 1555 2.24 LINK MG MG A 300 O HOH A 303 1555 1555 2.04 LINK MG MG A 300 O HOH A 304 1555 1555 2.02 LINK MG MG A 300 O HOH A 305 1555 1555 2.01 LINK MG MG A 300 O HOH A 306 1555 1555 2.06 LINK MG MG A 300 O HOH A 307 1555 1555 2.00 SITE 1 AC1 4 CYS A 126 CYS A 143 CYS A 207 HOH A 308 SITE 1 AC2 6 HOH A 302 HOH A 303 HOH A 304 HOH A 305 SITE 2 AC2 6 HOH A 306 HOH A 307 SITE 1 AC3 2 ARG A 103 HIS A 129 CRYST1 61.757 131.024 57.902 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 0.016192 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017271 0.00000 CONECT 360 369 CONECT 369 360 370 CONECT 370 369 371 373 CONECT 371 370 372 377 CONECT 372 371 CONECT 373 370 374 CONECT 374 373 375 CONECT 375 374 376 CONECT 376 375 CONECT 377 371 CONECT 417 423 CONECT 423 417 424 425 CONECT 424 423 426 428 CONECT 425 423 426 429 CONECT 426 424 425 427 436 CONECT 427 426 CONECT 428 424 430 CONECT 429 425 431 CONECT 430 428 432 CONECT 431 429 433 CONECT 432 430 434 CONECT 433 431 435 CONECT 434 432 CONECT 435 433 CONECT 436 426 CONECT 637 641 CONECT 641 637 642 CONECT 642 641 643 645 CONECT 643 642 644 649 CONECT 644 643 CONECT 645 642 646 CONECT 646 645 647 CONECT 647 646 648 CONECT 648 647 CONECT 649 643 CONECT 1019 1895 CONECT 1165 1895 CONECT 1199 1208 CONECT 1208 1199 1209 CONECT 1209 1208 1210 1212 CONECT 1210 1209 1211 1216 CONECT 1211 1210 CONECT 1212 1209 1213 CONECT 1213 1212 1214 CONECT 1214 1213 1215 CONECT 1215 1214 CONECT 1216 1210 CONECT 1341 1353 CONECT 1353 1341 1354 1355 CONECT 1354 1353 1356 1358 CONECT 1355 1353 1356 1359 CONECT 1356 1354 1355 1357 1366 CONECT 1357 1356 CONECT 1358 1354 1360 CONECT 1359 1355 1361 CONECT 1360 1358 1362 CONECT 1361 1359 1363 CONECT 1362 1360 1364 CONECT 1363 1361 1365 CONECT 1364 1362 CONECT 1365 1363 CONECT 1366 1356 CONECT 1418 1421 CONECT 1421 1418 1422 CONECT 1422 1421 1423 1425 CONECT 1423 1422 1424 1429 CONECT 1424 1423 CONECT 1425 1422 1426 CONECT 1426 1425 1427 CONECT 1427 1426 1428 CONECT 1428 1427 CONECT 1429 1423 CONECT 1666 1895 CONECT 1669 1674 CONECT 1674 1669 1675 CONECT 1675 1674 1676 1678 CONECT 1676 1675 1677 1682 CONECT 1677 1676 CONECT 1678 1675 1679 CONECT 1679 1678 1680 CONECT 1680 1679 1681 CONECT 1681 1680 CONECT 1682 1676 CONECT 1895 1019 1165 1666 1904 CONECT 1896 1898 1899 1900 1901 CONECT 1896 1902 1903 CONECT 1898 1896 CONECT 1899 1896 CONECT 1900 1896 CONECT 1901 1896 CONECT 1902 1896 CONECT 1903 1896 CONECT 1904 1895 MASTER 400 0 10 5 14 0 4 6 2113 1 93 18 END