HEADER ISOMERASE 08-JUL-09 3I7D TITLE CRYSTAL STRUCTURE OF SUGAR PHOSPHATE ISOMERASE FROM A CUPIN TITLE 2 SUPERFAMILY SPO2919 FROM SILICIBACTER POMEROYI (YP_168127.1) FROM TITLE 3 SILICIBACTER POMEROYI DSS-3 AT 2.30 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUGAR PHOSPHATE ISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RUEGERIA POMEROYI DSS-3; SOURCE 3 ORGANISM_TAXID: 246200; SOURCE 4 GENE: SPO2919, YP_168127.1; 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 YP_168127.1, SUGAR PHOSPHATE ISOMERASE FROM A CUPIN SUPERFAMILY KEYWDS 2 SPO2919 FROM SILICIBACTER POMEROYI, STRUCTURAL GENOMICS, JOINT KEYWDS 3 CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, KEYWDS 4 PSI-2, SUGAR METABOLISM, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3I7D 1 REMARK SEQADV REVDAT 4 24-JUL-19 3I7D 1 REMARK LINK REVDAT 3 01-NOV-17 3I7D 1 REMARK REVDAT 2 13-JUL-11 3I7D 1 VERSN REVDAT 1 21-JUL-09 3I7D 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF SUGAR PHOSPHATE ISOMERASE FROM A CUPIN JRNL TITL 2 SUPERFAMILY SPO2919 FROM SILICIBACTER POMEROYI (YP_168127.1) JRNL TITL 3 FROM SILICIBACTER POMEROYI DSS-3 AT 2.30 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 16826 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 850 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1120 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.50 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.2710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2378 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 179 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.40000 REMARK 3 B22 (A**2) : 0.40000 REMARK 3 B33 (A**2) : -0.80000 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): 0.310 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.230 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.173 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.302 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.906 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2443 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1658 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3303 ; 1.369 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4023 ; 0.886 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 313 ; 6.168 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;30.215 ;23.860 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 385 ;14.248 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;12.146 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 357 ; 0.076 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2780 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 492 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 449 ; 0.195 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1755 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1146 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1377 ; 0.085 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 160 ; 0.164 ; 0.200 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): 8 ; 0.108 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 27 ; 0.311 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.224 ; 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): 1839 ; 1.644 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 645 ; 0.357 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2493 ; 2.081 ; 4.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 959 ; 3.100 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 810 ; 4.001 ; 6.000 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 : 3 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 2 A 136 2 REMARK 3 1 B 2 B 136 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 787 ; 0.060 ; 0.050 REMARK 3 MEDIUM POSITIONAL 1 A (A): 948 ; 0.280 ; 0.500 REMARK 3 TIGHT THERMAL 1 A (A**2): 787 ; 0.180 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 948 ; 0.920 ; 2.000 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 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 137 A 142 4 REMARK 3 1 B 137 B 142 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 A (A): 71 ; 0.670 ; 0.500 REMARK 3 MEDIUM THERMAL 2 A (A**2): 71 ; 1.320 ; 2.000 REMARK 3 REMARK 3 NCS GROUP NUMBER : 3 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 143 A 158 2 REMARK 3 1 B 143 B 158 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 3 A (A): 93 ; 0.050 ; 0.050 REMARK 3 MEDIUM POSITIONAL 3 A (A): 107 ; 0.120 ; 0.500 REMARK 3 TIGHT THERMAL 3 A (A**2): 93 ; 0.130 ; 0.500 REMARK 3 MEDIUM THERMAL 3 A (A**2): 107 ; 0.530 ; 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 3. CHLORIDE (CL), CACODYLATE (CAC) AND ACETATE REMARK 3 (ACT) IONS, AND PEG8000 FRAGMENT(PEG) MOLECULES ARE MODELED REMARK 3 BASED ON CRYSTALLIZATION CONDITION. REMARK 4 REMARK 4 3I7D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-09. REMARK 100 THE DEPOSITION ID IS D_1000054056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.33 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) : 0.91837,0.97959,0.97941 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 : 16869 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 29.761 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.300 REMARK 200 R MERGE (I) : 0.33600 REMARK 200 R SYM (I) : 0.33600 REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 9.50 REMARK 200 R MERGE FOR SHELL (I) : 0.01200 REMARK 200 R SYM FOR SHELL (I) : 1.20400 REMARK 200 FOR SHELL : 0.600 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 (%): 49.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24.0000% POLYETHYLENE GLYCOL 8000, REMARK 280 0.3000M SODIUM ACETATE, 0.1M SODIUM CACODYLATE PH 6.33, NANODROP' REMARK 280 , VAPOR DIFFUSION, SITTING DROP, 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 126.08150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 26.40750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 26.40750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 63.04075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 26.40750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 26.40750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 189.12225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 26.40750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 26.40750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 63.04075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 26.40750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 26.40750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 189.12225 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 126.08150 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: 3680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 GLY A 0 REMARK 465 MSE A 1 REMARK 465 ASP A 159 REMARK 465 ASP A 160 REMARK 465 ASN A 161 REMARK 465 GLU A 162 REMARK 465 GLY B 0 REMARK 465 ASP B 159 REMARK 465 ASP B 160 REMARK 465 ASN B 161 REMARK 465 GLU B 162 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 ASP B 148 OG SER B 150 2.17 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 120 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 56 168.26 177.70 REMARK 500 SER B 56 165.98 176.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAC A 164 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAC B 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG B 164 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 391429 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 3I7D A 1 162 UNP Q5LPC9 Q5LPC9_SILPO 1 162 DBREF 3I7D B 1 162 UNP Q5LPC9 Q5LPC9_SILPO 1 162 SEQADV 3I7D GLY A 0 UNP Q5LPC9 EXPRESSION TAG SEQADV 3I7D GLY B 0 UNP Q5LPC9 EXPRESSION TAG SEQRES 1 A 163 GLY MSE PRO LYS LEU ASP LEU ASP SER ILE GLU ARG ARG SEQRES 2 A 163 ILE GLY SER VAL TYR PRO GLY ARG LEU ASN ALA ALA MSE SEQRES 3 A 163 ASP GLY ARG SER SER LEU ARG LEU GLY ASP ALA GLY GLY SEQRES 4 A 163 LEU SER GLN PHE GLY VAL ASN LEU VAL ARG LEU GLU PRO SEQRES 5 A 163 GLY ALA LYS SER SER LEU ARG HIS TYR HIS MSE GLU GLN SEQRES 6 A 163 ASP GLU PHE VAL MSE VAL THR GLU GLY ALA LEU VAL LEU SEQRES 7 A 163 VAL ASP ASP GLN GLY GLU HIS PRO MSE VAL PRO GLY ASP SEQRES 8 A 163 CYS ALA ALA PHE PRO ALA GLY ASP PRO ASN GLY HIS GLN SEQRES 9 A 163 PHE VAL ASN ARG THR ASP ALA PRO ALA THR PHE LEU VAL SEQRES 10 A 163 VAL GLY THR ARG THR PRO THR GLU THR ALA TYR TYR SER SEQRES 11 A 163 ASP MSE ASP MSE MSE VAL LYS GLN ASP ALA SER GLY PHE SEQRES 12 A 163 ALA PHE THR ARG LYS ASP GLY SER PRO LEU THR ALA ASP SEQRES 13 A 163 GLN ILE GLY ASP ASP ASN GLU SEQRES 1 B 163 GLY MSE PRO LYS LEU ASP LEU ASP SER ILE GLU ARG ARG SEQRES 2 B 163 ILE GLY SER VAL TYR PRO GLY ARG LEU ASN ALA ALA MSE SEQRES 3 B 163 ASP GLY ARG SER SER LEU ARG LEU GLY ASP ALA GLY GLY SEQRES 4 B 163 LEU SER GLN PHE GLY VAL ASN LEU VAL ARG LEU GLU PRO SEQRES 5 B 163 GLY ALA LYS SER SER LEU ARG HIS TYR HIS MSE GLU GLN SEQRES 6 B 163 ASP GLU PHE VAL MSE VAL THR GLU GLY ALA LEU VAL LEU SEQRES 7 B 163 VAL ASP ASP GLN GLY GLU HIS PRO MSE VAL PRO GLY ASP SEQRES 8 B 163 CYS ALA ALA PHE PRO ALA GLY ASP PRO ASN GLY HIS GLN SEQRES 9 B 163 PHE VAL ASN ARG THR ASP ALA PRO ALA THR PHE LEU VAL SEQRES 10 B 163 VAL GLY THR ARG THR PRO THR GLU THR ALA TYR TYR SER SEQRES 11 B 163 ASP MSE ASP MSE MSE VAL LYS GLN ASP ALA SER GLY PHE SEQRES 12 B 163 ALA PHE THR ARG LYS ASP GLY SER PRO LEU THR ALA ASP SEQRES 13 B 163 GLN ILE GLY ASP ASP ASN GLU MODRES 3I7D MSE A 25 MET SELENOMETHIONINE MODRES 3I7D MSE A 62 MET SELENOMETHIONINE MODRES 3I7D MSE A 69 MET SELENOMETHIONINE MODRES 3I7D MSE A 86 MET SELENOMETHIONINE MODRES 3I7D MSE A 131 MET SELENOMETHIONINE MODRES 3I7D MSE A 133 MET SELENOMETHIONINE MODRES 3I7D MSE A 134 MET SELENOMETHIONINE MODRES 3I7D MSE B 1 MET SELENOMETHIONINE MODRES 3I7D MSE B 25 MET SELENOMETHIONINE MODRES 3I7D MSE B 62 MET SELENOMETHIONINE MODRES 3I7D MSE B 69 MET SELENOMETHIONINE MODRES 3I7D MSE B 86 MET SELENOMETHIONINE MODRES 3I7D MSE B 131 MET SELENOMETHIONINE MODRES 3I7D MSE B 133 MET SELENOMETHIONINE MODRES 3I7D MSE B 134 MET SELENOMETHIONINE HET MSE A 25 8 HET MSE A 62 8 HET MSE A 69 8 HET MSE A 86 8 HET MSE A 131 8 HET MSE A 133 8 HET MSE A 134 8 HET MSE B 1 8 HET MSE B 25 8 HET MSE B 62 8 HET MSE B 69 8 HET MSE B 86 8 HET MSE B 131 8 HET MSE B 133 8 HET MSE B 134 8 HET CL A 163 1 HET CAC A 164 5 HET ACT A 165 4 HET CAC B 163 5 HET PEG B 164 7 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION HETNAM CAC CACODYLATE ION HETNAM ACT ACETATE ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN CAC DIMETHYLARSINATE FORMUL 1 MSE 15(C5 H11 N O2 SE) FORMUL 3 CL CL 1- FORMUL 4 CAC 2(C2 H6 AS O2 1-) FORMUL 5 ACT C2 H3 O2 1- FORMUL 7 PEG C4 H10 O3 FORMUL 8 HOH *179(H2 O) HELIX 1 1 PRO A 18 ASP A 26 5 9 HELIX 2 2 LEU A 33 GLY A 37 1 5 HELIX 3 3 THR A 153 GLY A 158 1 6 HELIX 4 4 PRO B 18 ASP B 26 5 9 HELIX 5 5 LEU B 33 GLY B 37 1 5 HELIX 6 6 THR B 153 GLY B 158 1 6 SHEET 1 A 6 ARG A 11 ILE A 13 0 SHEET 2 A 6 ARG A 28 ARG A 32 -1 O SER A 30 N ARG A 12 SHEET 3 A 6 PHE A 42 LEU A 49 -1 O ARG A 48 N SER A 29 SHEET 4 A 6 ALA A 112 THR A 119 -1 O ALA A 112 N LEU A 49 SHEET 5 A 6 GLU A 66 GLU A 72 -1 N PHE A 67 O VAL A 117 SHEET 6 A 6 CYS A 91 PHE A 94 -1 O PHE A 94 N GLU A 66 SHEET 1 B 4 HIS A 59 HIS A 61 0 SHEET 2 B 4 GLU A 124 TYR A 128 -1 O TYR A 127 N TYR A 60 SHEET 3 B 4 MSE A 133 GLN A 137 -1 O GLN A 137 N GLU A 124 SHEET 4 B 4 PHE A 142 THR A 145 -1 O THR A 145 N MSE A 134 SHEET 1 C 3 GLY A 82 MSE A 86 0 SHEET 2 C 3 LEU A 75 ASP A 79 -1 N LEU A 77 O HIS A 84 SHEET 3 C 3 GLN A 103 VAL A 105 -1 O GLN A 103 N VAL A 78 SHEET 1 D 6 ARG B 11 ILE B 13 0 SHEET 2 D 6 ARG B 28 ARG B 32 -1 O SER B 30 N ARG B 12 SHEET 3 D 6 PHE B 42 LEU B 49 -1 O ARG B 48 N SER B 29 SHEET 4 D 6 ALA B 112 THR B 119 -1 O ALA B 112 N LEU B 49 SHEET 5 D 6 GLU B 66 GLU B 72 -1 N MSE B 69 O LEU B 115 SHEET 6 D 6 CYS B 91 PHE B 94 -1 O PHE B 94 N GLU B 66 SHEET 1 E 4 HIS B 59 HIS B 61 0 SHEET 2 E 4 GLU B 124 TYR B 128 -1 O TYR B 127 N TYR B 60 SHEET 3 E 4 MSE B 134 ASP B 138 -1 O GLN B 137 N GLU B 124 SHEET 4 E 4 GLY B 141 THR B 145 -1 O ALA B 143 N LYS B 136 SHEET 1 F 3 GLY B 82 MSE B 86 0 SHEET 2 F 3 LEU B 75 ASP B 79 -1 N LEU B 77 O HIS B 84 SHEET 3 F 3 GLN B 103 VAL B 105 -1 O GLN B 103 N VAL B 78 LINK C ALA A 24 N MSE A 25 1555 1555 1.33 LINK C MSE A 25 N ASP A 26 1555 1555 1.34 LINK C HIS A 61 N MSE A 62 1555 1555 1.33 LINK C MSE A 62 N GLU A 63 1555 1555 1.33 LINK C VAL A 68 N MSE A 69 1555 1555 1.33 LINK C MSE A 69 N VAL A 70 1555 1555 1.34 LINK C PRO A 85 N MSE A 86 1555 1555 1.34 LINK C MSE A 86 N VAL A 87 1555 1555 1.34 LINK C ASP A 130 N MSE A 131 1555 1555 1.32 LINK C MSE A 131 N ASP A 132 1555 1555 1.33 LINK C ASP A 132 N MSE A 133 1555 1555 1.32 LINK C MSE A 133 N MSE A 134 1555 1555 1.32 LINK C MSE A 134 N VAL A 135 1555 1555 1.32 LINK C MSE B 1 N PRO B 2 1555 1555 1.36 LINK C ALA B 24 N MSE B 25 1555 1555 1.33 LINK C MSE B 25 N ASP B 26 1555 1555 1.33 LINK C HIS B 61 N MSE B 62 1555 1555 1.33 LINK C MSE B 62 N GLU B 63 1555 1555 1.32 LINK C VAL B 68 N MSE B 69 1555 1555 1.33 LINK C MSE B 69 N VAL B 70 1555 1555 1.33 LINK C PRO B 85 N MSE B 86 1555 1555 1.33 LINK C MSE B 86 N VAL B 87 1555 1555 1.32 LINK C ASP B 130 N MSE B 131 1555 1555 1.32 LINK C MSE B 131 N ASP B 132 1555 1555 1.33 LINK C ASP B 132 N MSE B 133 1555 1555 1.33 LINK C MSE B 133 N MSE B 134 1555 1555 1.32 LINK C MSE B 134 N VAL B 135 1555 1555 1.32 SITE 1 AC1 4 ASP A 132 GLN A 156 ASP B 132 GLN B 156 SITE 1 AC2 6 TYR A 17 HIS A 59 HIS A 61 TYR A 128 SITE 2 AC2 6 HOH A 181 HOH A 184 SITE 1 AC3 6 SER A 55 SER A 56 GLU A 66 HIS A 102 SITE 2 AC3 6 GLN A 103 HOH A 242 SITE 1 AC4 6 TYR B 17 HIS B 59 HIS B 61 TYR B 128 SITE 2 AC4 6 HOH B 188 HOH B 239 SITE 1 AC5 5 ASP B 26 GLY B 27 ARG B 28 HOH B 183 SITE 2 AC5 5 HOH B 206 CRYST1 52.815 52.815 252.163 90.00 90.00 90.00 P 41 21 2 16 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 0.018934 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018934 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003966 0.00000