HEADER SUGAR BINDING PROTEIN 22-SEP-09 3JYS TITLE CRYSTAL STRUCTURE OF SUSD SUPERFAMILY PROTEIN (YP_001298690.1) FROM TITLE 2 BACTEROIDES VULGATUS ATCC 8482 AT 2.00 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUSD SUPERFAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PUTATIVE OUTER MEMBRANE PROTEIN, PROBABLY INVOLVED IN COMPND 5 NUTRIENT BINDING; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACTEROIDES VULGATUS ATCC 8482; SOURCE 3 ORGANISM_TAXID: 435590; SOURCE 4 STRAIN: ATCC 8482 / DSM 1447 / NCTC 11154; SOURCE 5 GENE: BVU_1379, YP_001298690.1; 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_001298690.1, SUSD SUPERFAMILY PROTEIN, STRUCTURAL GENOMICS, JOINT KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 PSI-2, RAGB, SUSD AND HYPOTHETICAL PROTEINS, UNKNOWN FUNCTION, SUGAR KEYWDS 4 BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3JYS 1 REMARK SEQADV LINK REVDAT 4 24-JUL-19 3JYS 1 REMARK LINK REVDAT 3 01-NOV-17 3JYS 1 REMARK REVDAT 2 13-JUL-11 3JYS 1 VERSN REVDAT 1 06-OCT-09 3JYS 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF SUSD SUPERFAMILY PROTEIN JRNL TITL 2 (YP_001298690.1) FROM BACTEROIDES VULGATUS ATCC 8482 AT 2.00 JRNL TITL 3 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 38586 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1931 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2644 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2590 REMARK 3 BIN FREE R VALUE SET COUNT : 138 REMARK 3 BIN FREE R VALUE : 0.2560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3814 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 266 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 32.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.33000 REMARK 3 B22 (A**2) : 1.33000 REMARK 3 B33 (A**2) : -2.66000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.165 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.136 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.107 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.817 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4001 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2667 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5460 ; 1.476 ; 1.935 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6480 ; 0.967 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 505 ; 6.145 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 214 ;37.632 ;24.766 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 645 ;14.618 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ; 8.307 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 575 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4593 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 850 ; 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): 2422 ; 0.724 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 988 ; 0.198 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3902 ; 1.250 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1579 ; 2.046 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1543 ; 3.059 ; 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 38 A 62 REMARK 3 RESIDUE RANGE : A 79 A 535 REMARK 3 ORIGIN FOR THE GROUP (A): 57.3110 25.7700 119.8060 REMARK 3 T TENSOR REMARK 3 T11: 0.1833 T22: 0.1264 REMARK 3 T33: 0.1262 T12: -0.1092 REMARK 3 T13: 0.0318 T23: -0.0427 REMARK 3 L TENSOR REMARK 3 L11: 2.0743 L22: 0.6350 REMARK 3 L33: 2.2126 L12: -0.0264 REMARK 3 L13: 1.0421 L23: -0.0783 REMARK 3 S TENSOR REMARK 3 S11: 0.0462 S12: -0.2403 S13: 0.1970 REMARK 3 S21: 0.1126 S22: -0.1133 S23: 0.0460 REMARK 3 S31: -0.2615 S32: -0.1743 S33: 0.0670 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. ATOM RECORDS CONTAIN RESIDUAL B FACTORS REMARK 3 ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE REMARK 3 INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE REMARK 3 ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED REMARK 3 SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. REMARK 3 MAGNESIUM ION IS MODELED FROM CRYSTALLIZATION CONDITION. REMARK 4 REMARK 4 3JYS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055329. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91162,0.97936 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : FLAT COLLIMATING MIRROR, TOROID REMARK 200 FOCUSING MIRROR 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 3.2.5 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38690 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.111 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.64300 REMARK 200 R SYM FOR SHELL (I) : 0.64300 REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2000M MGCL2, 20.0000% PEG-3350, NO REMARK 280 BUFFER PH 5.8, NANODROP, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 133.19900 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.96450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.96450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 66.59950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.96450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.96450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 199.79850 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.96450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.96450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 66.59950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.96450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.96450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 199.79850 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 133.19900 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 SUGGESTS THE ASSIGNMENT OF A REMARK 300 MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. 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 0 REMARK 465 GLN A 63 REMARK 465 ASP A 64 REMARK 465 GLY A 65 REMARK 465 SER A 66 REMARK 465 SER A 67 REMARK 465 SER A 68 REMARK 465 SER A 69 REMARK 465 ASP A 70 REMARK 465 ILE A 71 REMARK 465 SER A 72 REMARK 465 GLY A 73 REMARK 465 LEU A 74 REMARK 465 ASP A 75 REMARK 465 ALA A 76 REMARK 465 GLY A 77 REMARK 465 ASN A 78 REMARK 465 LYS A 295 REMARK 465 THR A 296 REMARK 465 GLN A 297 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 39 CD CE NZ REMARK 470 GLU A 45 CD OE1 OE2 REMARK 470 LYS A 49 CD CE NZ REMARK 470 GLU A 152 CD OE1 OE2 REMARK 470 LYS A 258 CD CE NZ REMARK 470 TRP A 299 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 299 CZ3 CH2 REMARK 470 LYS A 349 CD CE NZ REMARK 470 LYS A 363 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD1 ASN A 391 OD1 ASN A 393 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 248 CD GLU A 248 OE1 0.070 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 THR A 42 -85.70 -144.71 REMARK 500 SER A 61 -71.48 -86.01 REMARK 500 THR A 114 -153.81 -124.69 REMARK 500 ALA A 174 -50.24 67.90 REMARK 500 TYR A 184 134.28 -39.30 REMARK 500 GLU A 217 114.31 -167.62 REMARK 500 ARG A 245 47.57 -143.83 REMARK 500 SER A 321 -8.20 -140.71 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 MG A 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 291 O REMARK 620 2 ASP A 404 O 92.9 REMARK 620 3 ASP A 406 OD1 93.0 91.6 REMARK 620 4 HOH A 729 O 107.9 158.9 83.7 REMARK 620 5 HOH A 738 O 89.9 98.8 169.0 85.3 REMARK 620 6 HOH A 740 O 175.4 82.7 88.2 76.6 89.7 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 MG A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 396550 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE 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 3JYS A 38 535 UNP A6L054 A6L054_BACV8 38 535 SEQADV 3JYS GLY A 0 UNP A6L054 EXPRESSION TAG SEQRES 1 A 499 GLY ASP LYS ALA TYR THR ASP ALA GLU SER TYR THR LYS SEQRES 2 A 499 GLY LEU HIS LYS ILE TYR SER VAL TRP ALA LEU SER GLY SEQRES 3 A 499 GLN ASP GLY SER SER SER SER ASP ILE SER GLY LEU ASP SEQRES 4 A 499 ALA GLY ASN THR ALA LEU LEU ARG CYS TRP TRP THR LEU SEQRES 5 A 499 GLN GLU GLN PRO THR ASP GLU MSE LYS ASN ALA TRP ASN SEQRES 6 A 499 ASP ALA TRP CYS THR GLU VAL ASN TYR MSE THR TRP THR SEQRES 7 A 499 THR ASN LYS VAL GLU PRO ILE GLU GLY VAL TYR GLN ARG SEQRES 8 A 499 CYS MSE TYR ILE VAL ALA LEU VAL ASN GLU PHE LEU LYS SEQRES 9 A 499 ASN ILE PRO ASN ALA PRO GLU SER ILE ASP LYS GLU SER SEQRES 10 A 499 TYR ILE ALA GLN ALA ARG PHE ASN ARG ALA PHE ALA TYR SEQRES 11 A 499 TYR VAL LEU MSE ASP MSE PHE ALA LEU PRO PRO PHE ILE SEQRES 12 A 499 THR GLU LYS ASN TYR SER ILE GLU PRO ALA PRO LEU SER SEQRES 13 A 499 ARG GLU ASP LEU PHE ASN TRP ILE GLU ALA GLU LEU ASN SEQRES 14 A 499 GLU ILE LYS PRO ASN LEU PRO SER PRO ARG SER GLU TYR SEQRES 15 A 499 GLY VAL ALA ASP GLN ALA VAL ALA SER ALA LEU LEU ALA SEQRES 16 A 499 ARG MSE TYR LEU ASN ALA GLU ILE TYR THR GLY LYS ALA SEQRES 17 A 499 ARG TYR THR GLU CYS ILE ASN ALA CYS ASN GLU VAL ILE SEQRES 18 A 499 LYS ALA GLY TYR GLN LEU ALA ASP ASN TYR ALA ASP LEU SEQRES 19 A 499 PHE LYS ALA ASP ASN GLY GLU ASN PRO ASP THR LYS LYS SEQRES 20 A 499 GLU ILE ILE TYR PRO ILE ILE PHE ASP GLY ASP LYS THR SEQRES 21 A 499 GLN SER TRP GLY MSE ALA ALA ILE ILE ILE GLY ALA ARG SEQRES 22 A 499 GLY ALA GLU ASP LYS ASP VAL LEU LEU ALA HIS SER GLY SEQRES 23 A 499 VAL ASP GLN GLY TRP ALA GLY PHE ARG ALA THR SER ASN SEQRES 24 A 499 LEU VAL HIS LEU PHE ASP PHE GLN ASN ASP GLU GLU PRO SEQRES 25 A 499 LYS ALA SER GLU ILE GLN ASP LYS ARG GLY ILE PHE TYR SEQRES 26 A 499 ASP LYS GLY ARG SER ILE ASP ILE THR SER SER VAL SER SEQRES 27 A 499 GLY THR PHE GLU THR GLU GLY TRP SER VAL PHE LYS PHE SEQRES 28 A 499 SER ASN LEU ASN SER ASN GLY GLN PRO GLY LYS ASN THR SEQRES 29 A 499 LEU TRP VAL ASP THR ASP PHE PRO MSE PHE ARG LEU GLY SEQRES 30 A 499 ASP ILE TYR LEU MSE TYR ALA GLU ALA VAL ALA ARG GLY SEQRES 31 A 499 GLY GLU GLY SER LYS ALA SER ALA VAL GLU TYR ILE ASN SEQRES 32 A 499 ALA LEU ARG LYS ARG ALA TYR GLY ASP ASP LYS HIS ASN SEQRES 33 A 499 ILE SER GLU ASN TRP LEU GLU GLU ASN ASN PHE ARG ASN SEQRES 34 A 499 LEU LEU ASP GLU ARG GLY ARG GLU LEU TYR TRP GLU GLY SEQRES 35 A 499 ILE ARG ARG THR ASP LEU VAL ARG PHE ASP LEU LEU THR SEQRES 36 A 499 SER GLY SER TYR THR TRP ASP PHE LYS GLY GLY ILE ASN SEQRES 37 A 499 THR GLY VAL GLY VAL ASN LYS ARG TYR ASN VAL TYR PRO SEQRES 38 A 499 ILE PRO VAL THR ASP LEU THR VAL ASN GLY ASN LEU GLN SEQRES 39 A 499 GLN ASN GLU GLY TYR MODRES 3JYS MSE A 96 MET SELENOMETHIONINE MODRES 3JYS MSE A 111 MET SELENOMETHIONINE MODRES 3JYS MSE A 129 MET SELENOMETHIONINE MODRES 3JYS MSE A 170 MET SELENOMETHIONINE MODRES 3JYS MSE A 172 MET SELENOMETHIONINE MODRES 3JYS MSE A 233 MET SELENOMETHIONINE MODRES 3JYS MSE A 301 MET SELENOMETHIONINE MODRES 3JYS MSE A 409 MET SELENOMETHIONINE MODRES 3JYS MSE A 418 MET SELENOMETHIONINE HET MSE A 96 8 HET MSE A 111 8 HET MSE A 129 8 HET MSE A 170 8 HET MSE A 172 13 HET MSE A 233 8 HET MSE A 301 8 HET MSE A 409 8 HET MSE A 418 8 HET MG A 1 1 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION FORMUL 1 MSE 9(C5 H11 N O2 SE) FORMUL 2 MG MG 2+ FORMUL 3 HOH *266(H2 O) HELIX 1 1 ASP A 43 VAL A 57 1 15 HELIX 2 2 ALA A 80 GLN A 91 1 12 HELIX 3 3 ASP A 102 MSE A 111 1 10 HELIX 4 4 VAL A 118 ILE A 142 1 25 HELIX 5 5 PRO A 143 ALA A 145 5 3 HELIX 6 6 ASP A 150 ALA A 174 1 25 HELIX 7 7 SER A 192 LYS A 208 1 17 HELIX 8 8 PRO A 209 LEU A 211 5 3 HELIX 9 9 ASP A 222 ASN A 236 1 15 HELIX 10 10 ASN A 236 GLY A 242 1 7 HELIX 11 11 ARG A 245 ALA A 259 1 15 HELIX 12 12 TYR A 267 LYS A 272 5 6 HELIX 13 13 ASN A 278 LYS A 283 1 6 HELIX 14 14 TRP A 299 GLY A 307 1 9 HELIX 15 15 ASP A 313 GLY A 322 1 10 HELIX 16 16 THR A 333 LEU A 339 1 7 HELIX 17 17 LYS A 349 ILE A 353 5 5 HELIX 18 18 LEU A 412 ARG A 425 1 14 HELIX 19 19 SER A 430 GLY A 447 1 18 HELIX 20 20 SER A 454 GLU A 460 1 7 HELIX 21 21 PHE A 463 TYR A 475 1 13 HELIX 22 22 ILE A 479 PHE A 487 1 9 HELIX 23 23 PHE A 499 ILE A 503 5 5 HELIX 24 24 ASN A 510 VAL A 515 5 6 HELIX 25 25 PRO A 519 ASN A 526 1 8 SHEET 1 A 2 LYS A 97 ASN A 98 0 SHEET 2 A 2 PHE A 330 ARG A 331 -1 O ARG A 331 N LYS A 97 SHEET 1 B 2 ILE A 285 ILE A 289 0 SHEET 2 B 2 PHE A 407 ARG A 411 -1 O PHE A 407 N ILE A 289 SHEET 1 C 2 PHE A 360 TYR A 361 0 SHEET 2 C 2 SER A 383 VAL A 384 -1 O SER A 383 N TYR A 361 LINK C GLU A 95 N MSE A 96 1555 1555 1.32 LINK C MSE A 96 N LYS A 97 1555 1555 1.33 LINK C TYR A 110 N MSE A 111 1555 1555 1.34 LINK C MSE A 111 N THR A 112 1555 1555 1.32 LINK C CYS A 128 N MSE A 129 1555 1555 1.34 LINK C MSE A 129 N TYR A 130 1555 1555 1.33 LINK C LEU A 169 N MSE A 170 1555 1555 1.33 LINK C MSE A 170 N ASP A 171 1555 1555 1.32 LINK C ASP A 171 N MSE A 172 1555 1555 1.32 LINK C MSE A 172 N PHE A 173 1555 1555 1.34 LINK C ARG A 232 N MSE A 233 1555 1555 1.32 LINK C MSE A 233 N TYR A 234 1555 1555 1.33 LINK C GLY A 300 N MSE A 301 1555 1555 1.33 LINK C MSE A 301 N ALA A 302 1555 1555 1.34 LINK C PRO A 408 N MSE A 409 1555 1555 1.33 LINK C MSE A 409 N PHE A 410 1555 1555 1.36 LINK C LEU A 417 N MSE A 418 1555 1555 1.32 LINK C MSE A 418 N TYR A 419 1555 1555 1.34 LINK MG MG A 1 O PHE A 291 1555 1555 1.85 LINK MG MG A 1 O ASP A 404 1555 1555 2.00 LINK MG MG A 1 OD1 ASP A 406 1555 1555 2.19 LINK MG MG A 1 O HOH A 729 1555 1555 2.17 LINK MG MG A 1 O HOH A 738 1555 1555 2.25 LINK MG MG A 1 O HOH A 740 1555 1555 1.97 SITE 1 AC1 6 PHE A 291 ASP A 404 ASP A 406 HOH A 729 SITE 2 AC1 6 HOH A 738 HOH A 740 CRYST1 63.929 63.929 266.398 90.00 90.00 90.00 P 41 21 2 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 0.015642 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015642 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003754 0.00000