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 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