HEADER METAL BINDING PROTEIN 19-JUN-08 3DI4 TITLE CRYSTAL STRUCTURE OF A DUF1989 FAMILY PROTEIN (SPO0365) FROM TITLE 2 SILICIBACTER POMEROYI DSS-3 AT 1.60 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN DUF1989; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SILICIBACTER POMEROYI; SOURCE 3 ORGANISM_TAXID: 246200; SOURCE 4 STRAIN: DSS-3; SOURCE 5 ATCC: 700808; SOURCE 6 GENE: YP_165628.1, SPO0365; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-2, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 8 09-OCT-24 3DI4 1 REMARK REVDAT 7 01-FEB-23 3DI4 1 REMARK SEQADV LINK REVDAT 6 24-JUL-19 3DI4 1 REMARK LINK REVDAT 5 25-OCT-17 3DI4 1 REMARK REVDAT 4 13-JUL-11 3DI4 1 VERSN REVDAT 3 23-MAR-11 3DI4 1 HEADER TITLE KEYWDS REVDAT 2 24-FEB-09 3DI4 1 VERSN REVDAT 1 01-JUL-08 3DI4 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PROTEIN OF UNKNOWN FUNCTION (DUF1989) JRNL TITL 2 (YP_165628.1) FROM SILICIBACTER POMEROYI DSS-3 AT 1.60 A JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 69445 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) : 0.142 REMARK 3 R VALUE (WORKING SET) : 0.141 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3499 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4622 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.2090 REMARK 3 BIN FREE R VALUE SET COUNT : 244 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4245 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 739 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.24000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.077 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.079 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.049 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.367 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4487 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3033 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6134 ; 1.539 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7358 ; 0.989 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 586 ; 6.127 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 210 ;32.066 ;22.762 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 672 ;11.904 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;15.417 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 659 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5142 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 958 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 925 ; 0.205 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3382 ; 0.210 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2163 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2323 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 562 ; 0.173 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.145 ; 0.200 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): 15 ; 0.217 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 30 ; 0.306 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 27 ; 0.195 ; 0.200 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): 2862 ; 1.616 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1141 ; 0.570 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4521 ; 2.302 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1809 ; 3.317 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1595 ; 4.587 ;11.000 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 8 A 291 4 REMARK 3 1 B 8 B 291 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 3571 ; 0.180 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 3571 ; 0.810 ; 2.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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: REMARK 3 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY REMARK 3 OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 REMARK 3 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. REMARK 3 3. ZN IS MODELED BASED ON AN X-RAY FLOURESCENCE SCAN, REMARK 3 ANOMALOUS DIFFERENCE FOURIERS, AND COORDINATION GEOMETRY. REMARK 3 4. A SULFATE (SO4) ION, A GLYCEROL (GOL) MOLECULE AND FOUR REMARK 3 CHLORIDE IONS ARE MODELED BASED ON CRYSTALLIZATION CONDITIONS, REMARK 3 ELECTRON DENSITY AND COORDINATION GEOMETRY. REMARK 4 REMARK 4 3DI4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000048065. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 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) : 0.91837,0.97941,0.97904 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 69473 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 28.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.44400 REMARK 200 R SYM FOR SHELL (I) : 0.44400 REMARK 200 FOR SHELL : 1.700 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 (%): 43.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.7M AMMONIUM SULFATE, 2.0% REMARK 280 POLYETHYLENE GLYCOL 400, 15.0% GLYCEROL, 0.1M HEPES PH 6.9, REMARK 280 NANODROP', VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 47.88200 REMARK 290 SMTRY3 2 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: 9540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -181.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 HIS A 246 REMARK 465 SER A 247 REMARK 465 SER A 248 REMARK 465 ASP A 249 REMARK 465 THR A 250 REMARK 465 GLY B 0 REMARK 465 MSE B 1 REMARK 465 THR B 2 REMARK 465 ASP B 3 REMARK 465 ALA B 4 REMARK 465 PRO B 5 REMARK 465 ALA B 6 REMARK 465 HIS B 246 REMARK 465 SER B 247 REMARK 465 SER B 248 REMARK 465 ASP B 249 REMARK 465 THR B 250 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 ARG A 31 CD NE CZ NH1 NH2 REMARK 470 ARG A 45 CD NE CZ NH1 NH2 REMARK 470 GLU A 245 CG CD OE1 OE2 REMARK 470 ASP B 7 N CA CB CG OD1 OD2 REMARK 470 ARG B 31 NE CZ NH1 NH2 REMARK 470 ARG B 45 CD NE CZ NH1 NH2 REMARK 470 LYS B 63 CE NZ REMARK 470 GLU B 245 CG CD OE1 OE2 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 43 CB SER A 43 OG 0.084 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 99 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 99 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 16 NE - CZ - NH1 ANGL. DEV. = 3.2 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 GLU A 74 -47.33 78.53 REMARK 500 GLU A 74 -43.37 75.26 REMARK 500 ASP A 88 88.15 -162.78 REMARK 500 LEU A 119 81.63 12.81 REMARK 500 HIS A 143 70.48 74.77 REMARK 500 ARG A 149 141.77 144.52 REMARK 500 PHE A 197 -7.26 75.84 REMARK 500 GLU B 74 -46.77 69.10 REMARK 500 ASP B 88 93.12 -161.42 REMARK 500 LEU B 119 81.12 16.03 REMARK 500 HIS B 143 73.02 72.59 REMARK 500 ARG B 149 139.52 145.17 REMARK 500 PHE B 197 -9.03 76.78 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 286 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 150 SG REMARK 620 2 CYS A 167 SG 113.7 REMARK 620 3 CYS A 237 SG 115.2 108.0 REMARK 620 4 HOH A 294 O 104.9 103.2 111.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 286 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 150 SG REMARK 620 2 CYS B 167 SG 114.2 REMARK 620 3 CYS B 237 SG 115.2 109.0 REMARK 620 4 HOH B 295 O 103.3 102.6 111.7 REMARK 620 N 1 2 3 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 286 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 286 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 288 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 287 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 289 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 288 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 289 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 383110 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 3DI4 A 1 285 UNP Q5LXE3 Q5LXE3_SILPO 1 285 DBREF 3DI4 B 1 285 UNP Q5LXE3 Q5LXE3_SILPO 1 285 SEQADV 3DI4 GLY A 0 UNP Q5LXE3 EXPRESSION TAG SEQADV 3DI4 GLY B 0 UNP Q5LXE3 EXPRESSION TAG SEQRES 1 A 286 GLY MSE THR ASP ALA PRO ALA ASP ALA PRO LEU ASP ALA SEQRES 2 A 286 ASP ALA ARG ARG ALA VAL LYS PRO VAL ILE CYS TYR PRO SEQRES 3 A 286 ASN ASP SER LEU PRO ARG PRO ASP LEU ALA LEU TYR ARG SEQRES 4 A 286 ALA ALA ARG ALA SER ALA ARG LYS THR GLY GLU VAL LEU SEQRES 5 A 286 VAL PRO PRO ARG GLU GLY ARG CYS PHE GLU VAL LYS ALA SEQRES 6 A 286 GLY GLN PHE PHE ARG ILE SER SER VAL GLU GLY PRO GLN SEQRES 7 A 286 VAL GLY ASP LEU ASN LEU HIS ASN LEU HIS ASP LEU THR SEQRES 8 A 286 GLU ARG PHE PHE SER GLY LYS THR ARG ALA LEU HIS GLY SEQRES 9 A 286 THR HIS VAL THR THR GLY GLU ARG LEU TRP SER ASN LEU SEQRES 10 A 286 PRO TYR LEU ARG PRO MSE ALA THR ILE ILE GLU ASP THR SEQRES 11 A 286 LEU GLY TRP TYR GLY ILE ASP GLN TYR GLY GLY SER VAL SEQRES 12 A 286 HIS ASP VAL ILE GLY THR ARG CYS ASP PRO TYR THR GLY SEQRES 13 A 286 ASN LEU LEU ALA GLY GLY HIS TYR HIS HIS CYS CYS HIS SEQRES 14 A 286 SER ASN LEU THR ARG ALA LEU ALA ASP HIS THR GLY LEU SEQRES 15 A 286 PRO LEU HIS GLU ALA GLU MSE LEU VAL HIS ASP VAL LEU SEQRES 16 A 286 ASN VAL PHE MSE CYS THR GLY PHE THR ARG ASP THR GLY SEQRES 17 A 286 GLN TYR PHE MSE LYS ALA SER PRO VAL ARG PRO GLY ASP SEQRES 18 A 286 TYR LEU GLU PHE PHE ALA GLU ILE ASP LEU LEU GLY ASN SEQRES 19 A 286 LEU SER ALA CYS PRO GLY GLY ASP CYS SER SER GLU HIS SEQRES 20 A 286 SER SER ASP THR ALA SER CYS HIS PRO LEU LEU VAL GLU SEQRES 21 A 286 ILE PHE ALA PRO ALA GLU GLY MSE LEU GLY ASP TRP PRO SEQRES 22 A 286 SER PRO SER VAL ASN GLY TYR ASP ARG SER HIS GLY ARG SEQRES 1 B 286 GLY MSE THR ASP ALA PRO ALA ASP ALA PRO LEU ASP ALA SEQRES 2 B 286 ASP ALA ARG ARG ALA VAL LYS PRO VAL ILE CYS TYR PRO SEQRES 3 B 286 ASN ASP SER LEU PRO ARG PRO ASP LEU ALA LEU TYR ARG SEQRES 4 B 286 ALA ALA ARG ALA SER ALA ARG LYS THR GLY GLU VAL LEU SEQRES 5 B 286 VAL PRO PRO ARG GLU GLY ARG CYS PHE GLU VAL LYS ALA SEQRES 6 B 286 GLY GLN PHE PHE ARG ILE SER SER VAL GLU GLY PRO GLN SEQRES 7 B 286 VAL GLY ASP LEU ASN LEU HIS ASN LEU HIS ASP LEU THR SEQRES 8 B 286 GLU ARG PHE PHE SER GLY LYS THR ARG ALA LEU HIS GLY SEQRES 9 B 286 THR HIS VAL THR THR GLY GLU ARG LEU TRP SER ASN LEU SEQRES 10 B 286 PRO TYR LEU ARG PRO MSE ALA THR ILE ILE GLU ASP THR SEQRES 11 B 286 LEU GLY TRP TYR GLY ILE ASP GLN TYR GLY GLY SER VAL SEQRES 12 B 286 HIS ASP VAL ILE GLY THR ARG CYS ASP PRO TYR THR GLY SEQRES 13 B 286 ASN LEU LEU ALA GLY GLY HIS TYR HIS HIS CYS CYS HIS SEQRES 14 B 286 SER ASN LEU THR ARG ALA LEU ALA ASP HIS THR GLY LEU SEQRES 15 B 286 PRO LEU HIS GLU ALA GLU MSE LEU VAL HIS ASP VAL LEU SEQRES 16 B 286 ASN VAL PHE MSE CYS THR GLY PHE THR ARG ASP THR GLY SEQRES 17 B 286 GLN TYR PHE MSE LYS ALA SER PRO VAL ARG PRO GLY ASP SEQRES 18 B 286 TYR LEU GLU PHE PHE ALA GLU ILE ASP LEU LEU GLY ASN SEQRES 19 B 286 LEU SER ALA CYS PRO GLY GLY ASP CYS SER SER GLU HIS SEQRES 20 B 286 SER SER ASP THR ALA SER CYS HIS PRO LEU LEU VAL GLU SEQRES 21 B 286 ILE PHE ALA PRO ALA GLU GLY MSE LEU GLY ASP TRP PRO SEQRES 22 B 286 SER PRO SER VAL ASN GLY TYR ASP ARG SER HIS GLY ARG MODRES 3DI4 MSE A 1 MET SELENOMETHIONINE MODRES 3DI4 MSE A 122 MET SELENOMETHIONINE MODRES 3DI4 MSE A 188 MET SELENOMETHIONINE MODRES 3DI4 MSE A 198 MET SELENOMETHIONINE MODRES 3DI4 MSE A 211 MET SELENOMETHIONINE MODRES 3DI4 MSE A 267 MET SELENOMETHIONINE MODRES 3DI4 MSE B 122 MET SELENOMETHIONINE MODRES 3DI4 MSE B 188 MET SELENOMETHIONINE MODRES 3DI4 MSE B 198 MET SELENOMETHIONINE MODRES 3DI4 MSE B 211 MET SELENOMETHIONINE MODRES 3DI4 MSE B 267 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 122 8 HET MSE A 188 8 HET MSE A 198 8 HET MSE A 211 8 HET MSE A 267 8 HET MSE B 122 8 HET MSE B 188 8 HET MSE B 198 8 HET MSE B 211 8 HET MSE B 267 8 HET ZN A 286 1 HET CL A 287 1 HET CL A 288 1 HET GOL A 289 6 HET ZN B 286 1 HET SO4 B 287 5 HET CL B 288 1 HET CL B 289 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 3 ZN 2(ZN 2+) FORMUL 4 CL 4(CL 1-) FORMUL 6 GOL C3 H8 O3 FORMUL 8 SO4 O4 S 2- FORMUL 11 HOH *739(H2 O) HELIX 1 1 ASP A 11 VAL A 18 1 8 HELIX 2 2 PRO A 25 LEU A 29 5 5 HELIX 3 3 ASP A 33 SER A 43 1 11 HELIX 4 4 PHE A 94 GLY A 103 1 10 HELIX 5 5 ASP A 151 GLY A 160 1 10 HELIX 6 6 CYS A 166 GLY A 180 1 15 HELIX 7 7 PRO A 182 MSE A 188 1 7 HELIX 8 8 ASP B 11 VAL B 18 1 8 HELIX 9 9 PRO B 25 LEU B 29 5 5 HELIX 10 10 ASP B 33 SER B 43 1 11 HELIX 11 11 PHE B 94 GLY B 103 1 10 HELIX 12 12 ASP B 151 GLY B 160 1 10 HELIX 13 13 CYS B 166 GLY B 180 1 15 HELIX 14 14 PRO B 182 VAL B 190 1 9 SHEET 1 A 5 VAL A 21 ILE A 22 0 SHEET 2 A 5 TYR B 209 LYS B 212 -1 O MSE B 211 N VAL A 21 SHEET 3 A 5 LEU B 194 PHE B 202 -1 N GLY B 201 O PHE B 210 SHEET 4 A 5 GLY B 79 ASN B 85 -1 N LEU B 81 O LEU B 194 SHEET 5 A 5 ASP B 88 ARG B 92 -1 O GLU B 91 N ASN B 85 SHEET 1 B 5 GLY B 57 VAL B 62 0 SHEET 2 B 5 LEU B 230 ALA B 236 -1 O GLY B 232 N PHE B 60 SHEET 3 B 5 GLY B 79 ASN B 85 -1 N ASN B 82 O ASN B 233 SHEET 4 B 5 LEU B 194 PHE B 202 -1 O LEU B 194 N LEU B 81 SHEET 5 B 5 SER B 141 ASP B 144 -1 N ASP B 144 O ASN B 195 SHEET 1 C 6 ARG A 45 VAL A 52 0 SHEET 2 C 6 LEU A 256 ALA A 262 -1 O ALA A 262 N ARG A 45 SHEET 3 C 6 PHE A 67 SER A 72 -1 N SER A 71 O LEU A 257 SHEET 4 C 6 TYR A 221 ALA A 226 -1 O PHE A 224 N PHE A 68 SHEET 5 C 6 PRO A 121 ASP A 128 -1 N THR A 124 O PHE A 225 SHEET 6 C 6 ARG A 111 TRP A 113 -1 N LEU A 112 O MSE A 122 SHEET 1 D 5 GLY A 57 VAL A 62 0 SHEET 2 D 5 LEU A 230 ALA A 236 -1 O LEU A 230 N VAL A 62 SHEET 3 D 5 GLY A 79 ASN A 85 -1 N ASN A 82 O ASN A 233 SHEET 4 D 5 LEU A 194 PHE A 202 -1 O LEU A 194 N LEU A 81 SHEET 5 D 5 SER A 141 ASP A 144 -1 N ASP A 144 O ASN A 195 SHEET 1 E 5 ASP A 88 ARG A 92 0 SHEET 2 E 5 GLY A 79 ASN A 85 -1 N ASN A 85 O GLU A 91 SHEET 3 E 5 LEU A 194 PHE A 202 -1 O LEU A 194 N LEU A 81 SHEET 4 E 5 TYR A 209 LYS A 212 -1 O PHE A 210 N GLY A 201 SHEET 5 E 5 VAL B 21 ILE B 22 -1 O VAL B 21 N MSE A 211 SHEET 1 F 6 ARG B 45 VAL B 52 0 SHEET 2 F 6 LEU B 256 ALA B 262 -1 O LEU B 256 N VAL B 52 SHEET 3 F 6 PHE B 67 SER B 72 -1 N ARG B 69 O GLU B 259 SHEET 4 F 6 TYR B 221 ALA B 226 -1 O PHE B 224 N PHE B 68 SHEET 5 F 6 PRO B 121 ASP B 128 -1 N GLU B 127 O GLU B 223 SHEET 6 F 6 ARG B 111 TRP B 113 -1 N LEU B 112 O MSE B 122 LINK C GLY A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N THR A 2 1555 1555 1.33 LINK C PRO A 121 N MSE A 122 1555 1555 1.33 LINK C MSE A 122 N ALA A 123 1555 1555 1.34 LINK C GLU A 187 N MSE A 188 1555 1555 1.33 LINK C MSE A 188 N LEU A 189 1555 1555 1.33 LINK C PHE A 197 N MSE A 198 1555 1555 1.32 LINK C MSE A 198 N CYS A 199 1555 1555 1.34 LINK C PHE A 210 N MSE A 211 1555 1555 1.33 LINK C MSE A 211 N LYS A 212 1555 1555 1.33 LINK C GLY A 266 N MSE A 267 1555 1555 1.32 LINK C MSE A 267 N LEU A 268 1555 1555 1.33 LINK C PRO B 121 N MSE B 122 1555 1555 1.34 LINK C MSE B 122 N ALA B 123 1555 1555 1.34 LINK C GLU B 187 N MSE B 188 1555 1555 1.32 LINK C MSE B 188 N LEU B 189 1555 1555 1.34 LINK C PHE B 197 N MSE B 198 1555 1555 1.33 LINK C MSE B 198 N CYS B 199 1555 1555 1.32 LINK C PHE B 210 N MSE B 211 1555 1555 1.33 LINK C MSE B 211 N LYS B 212 1555 1555 1.33 LINK C GLY B 266 N MSE B 267 1555 1555 1.33 LINK C MSE B 267 N LEU B 268 1555 1555 1.32 LINK SG CYS A 150 ZN ZN A 286 1555 1555 2.34 LINK SG CYS A 167 ZN ZN A 286 1555 1555 2.35 LINK SG CYS A 237 ZN ZN A 286 1555 1555 2.35 LINK ZN ZN A 286 O HOH A 294 1555 1555 2.07 LINK SG CYS B 150 ZN ZN B 286 1555 1555 2.31 LINK SG CYS B 167 ZN ZN B 286 1555 1555 2.33 LINK SG CYS B 237 ZN ZN B 286 1555 1555 2.34 LINK ZN ZN B 286 O HOH B 295 1555 1555 2.14 CISPEP 1 LEU A 116 PRO A 117 0 4.41 CISPEP 2 LEU B 116 PRO B 117 0 2.83 SITE 1 AC1 3 CYS A 150 CYS A 167 CYS A 237 SITE 1 AC2 3 CYS B 150 CYS B 167 CYS B 237 SITE 1 AC3 6 TYR A 24 LYS A 97 ALA A 100 THR B 148 SITE 2 AC3 6 ARG B 149 TYR B 209 SITE 1 AC4 2 HIS A 164 GLY B 161 SITE 1 AC5 3 THR A 148 ARG A 149 LYS B 97 SITE 1 AC6 2 ARG B 55 CYS B 253 SITE 1 AC7 2 GLY A 161 HIS B 164 SITE 1 AC8 3 PRO A 218 GLY A 219 ASP A 220 CRYST1 51.465 95.764 58.689 90.00 109.04 90.00 P 1 21 1 4 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 0.019431 0.000000 0.006707 0.00000 SCALE2 0.000000 0.010442 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018025 0.00000