HEADER HYDROLASE 01-JUN-10 3NA6 TITLE CRYSTAL STRUCTURE OF A SUCCINYLGLUTAMATE DESUCCINYLASE (TM1040_2694) TITLE 2 FROM SILICIBACTER SP. TM1040 AT 2.00 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUCCINYLGLUTAMATE DESUCCINYLASE/ASPARTOACYLASE; 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_2694; 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-2, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 4 01-FEB-23 3NA6 1 REMARK SEQADV LINK REVDAT 3 17-JUL-19 3NA6 1 REMARK LINK REVDAT 2 08-NOV-17 3NA6 1 REMARK REVDAT 1 28-JUL-10 3NA6 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A SUCCINYLGLUTAMATE DESUCCINYLASE JRNL TITL 2 (TM1040_2694) FROM SILICIBACTER SP. TM1040 AT 2.00 A JRNL TITL 3 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 5.5.0110 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 27844 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1397 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) : 1846 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.2540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2493 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 313 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.03 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.56 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.92000 REMARK 3 B22 (A**2) : 0.92000 REMARK 3 B33 (A**2) : -1.38000 REMARK 3 B12 (A**2) : 0.46000 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): 0.131 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.725 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2650 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1787 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3611 ; 1.513 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4353 ; 0.894 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 346 ; 6.526 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;35.242 ;23.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 424 ;14.023 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;24.762 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 396 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3049 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 542 ; 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): 1690 ; 1.724 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 687 ; 0.496 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2728 ; 2.817 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 960 ; 5.160 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 883 ; 7.279 ;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 : 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 : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 329 REMARK 3 ORIGIN FOR THE GROUP (A): 31.6428 11.7766 18.1997 REMARK 3 T TENSOR REMARK 3 T11: 0.0272 T22: 0.0194 REMARK 3 T33: 0.0177 T12: -0.0010 REMARK 3 T13: 0.0036 T23: -0.0181 REMARK 3 L TENSOR REMARK 3 L11: 0.1511 L22: 0.2766 REMARK 3 L33: 0.5690 L12: -0.1290 REMARK 3 L13: -0.0362 L23: 0.2195 REMARK 3 S TENSOR REMARK 3 S11: 0.0011 S12: 0.0131 S13: -0.0178 REMARK 3 S21: -0.0394 S22: -0.0487 S23: 0.0426 REMARK 3 S31: 0.0179 S32: -0.0621 S33: 0.0476 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: (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) ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL REMARK 3 B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U REMARK 3 FACTORS.(4) WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. REMARK 3 (5) CHLORIDE (CL), CALCIUM (CA) AND TRIS (TRS) IONS ARE MODELED REMARK 3 FROM CRYSTALLIZATION CONDITION. (6) REGION OF RESIDUES 251-256 REMARK 3 CONTAINS POOR ELECTRON DENSITY. MODEL AT THIS REGION IS NOT REMARK 3 RELIABLE. REMARK 4 REMARK 4 3NA6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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) : 0.91837,0.97922,0.97905 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27876 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.487 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.15700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5600 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) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.01300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2000M NACL, 30.0000% PEG-3000, 0.1M REMARK 280 TRIS PH 7.0, 0.006 M CALCIUM CHLORIDE, NANODROP, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 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 68.58950 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 68.58950 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 68.58950 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 68.58950 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 68.58950 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 68.58950 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 22300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 67490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -188.0 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 -0.500000 -0.866025 0.000000 99.77300 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 49.88650 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 86.40595 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 49.88650 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 86.40595 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 68.58950 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 99.77300 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 68.58950 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 68.58950 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 631 LIES ON A SPECIAL POSITION. 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 GLY A 330 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 2 CD CE NZ REMARK 470 ILE A 188 CG1 CG2 CD1 REMARK 470 GLU A 191 OE1 OE2 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 31 96.82 -164.32 REMARK 500 ASP A 189 58.69 -102.74 REMARK 500 MSE A 252 95.91 -39.38 REMARK 500 LEU A 259 69.85 -111.83 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 CA A 332 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 81 OG1 REMARK 620 2 GLY A 236 O 67.7 REMARK 620 3 HOH A 434 O 82.4 78.9 REMARK 620 4 HOH A 565 O 159.7 98.1 80.6 REMARK 620 5 HOH A 567 O 92.2 157.6 89.1 98.5 REMARK 620 6 HOH A 568 O 108.7 94.5 164.0 86.1 101.6 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 CL A 331 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 332 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 333 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 375176 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 3NA6 A 1 330 UNP Q1GD40 Q1GD40_SILST 1 330 SEQADV 3NA6 GLY A 0 UNP Q1GD40 EXPRESSION TAG SEQRES 1 A 331 GLY MSE LYS ASP ASN PRO ILE SER PRO THR ILE PRO LEU SEQRES 2 A 331 ASP GLN ASP GLY VAL HIS HIS GLY PHE LEU LYS LEU PRO SEQRES 3 A 331 TYR SER ARG ASP ASP SER ALA TRP GLY SER VAL MSE ILE SEQRES 4 A 331 PRO ILE THR VAL ILE GLN ASN GLY ALA GLY LYS THR ALA SEQRES 5 A 331 LEU LEU THR GLY ALA ASN HIS GLY ASP GLU TYR GLU GLY SEQRES 6 A 331 PRO VAL ALA LEU GLN GLU LEU ALA ALA THR THR ARG ALA SEQRES 7 A 331 GLU ASP VAL THR GLY ARG LEU ILE ILE VAL PRO TYR PHE SEQRES 8 A 331 ASN TYR PRO ALA PHE ARG ALA SER ALA ARG THR SER PRO SEQRES 9 A 331 ILE ASP ARG GLY ASN LEU ASN ARG ALA PHE PRO GLY ARG SEQRES 10 A 331 PRO ASP GLY THR VAL THR GLN LYS ILE ALA ASP TYR PHE SEQRES 11 A 331 GLN ARG THR LEU LEU PRO MSE ALA ASP VAL ALA VAL ASP SEQRES 12 A 331 PHE HIS SER GLY GLY LYS THR LEU ASP PHE VAL PRO PHE SEQRES 13 A 331 ALA ALA ALA HIS ILE LEU GLU ASP LYS VAL LEU GLN ASP SEQRES 14 A 331 ALA CYS PHE ALA ALA MSE GLN ALA PHE ASN ALA PRO TYR SEQRES 15 A 331 SER VAL GLN LEU LEU GLU ILE ASP SER GLU GLY MSE TYR SEQRES 16 A 331 ASP THR ALA VAL GLU GLU MSE GLY LYS VAL LEU VAL THR SEQRES 17 A 331 THR GLU LEU GLY GLY GLY GLY MSE SER THR ALA ARG SER SEQRES 18 A 331 ASN ALA ILE ALA LYS LYS GLY LEU ARG ASN VAL LEU ILE SEQRES 19 A 331 HIS PHE GLY ILE LEU GLN GLY GLU MSE GLN ILE ASP PRO SEQRES 20 A 331 SER VAL THR LEU ASP MSE PRO ASP GLY ASP CYS TYR LEU SEQRES 21 A 331 PHE SER GLU HIS ASP GLY LEU PHE GLU ILE MSE ILE ASP SEQRES 22 A 331 LEU GLY GLU PRO VAL GLN GLU GLY ASP LEU VAL ALA ARG SEQRES 23 A 331 VAL TRP SER PRO ASP ARG THR GLY GLU ALA PRO VAL GLU SEQRES 24 A 331 TYR ARG ALA ARG ARG SER GLY VAL LEU ILE SER ARG HIS SEQRES 25 A 331 PHE PRO GLY MSE ILE LYS SER GLY ASP CYS ALA ALA VAL SEQRES 26 A 331 ILE GLY VAL VAL GLU GLY MODRES 3NA6 MSE A 1 MET SELENOMETHIONINE MODRES 3NA6 MSE A 37 MET SELENOMETHIONINE MODRES 3NA6 MSE A 136 MET SELENOMETHIONINE MODRES 3NA6 MSE A 174 MET SELENOMETHIONINE MODRES 3NA6 MSE A 193 MET SELENOMETHIONINE MODRES 3NA6 MSE A 201 MET SELENOMETHIONINE MODRES 3NA6 MSE A 215 MET SELENOMETHIONINE MODRES 3NA6 MSE A 242 MET SELENOMETHIONINE MODRES 3NA6 MSE A 252 MET SELENOMETHIONINE MODRES 3NA6 MSE A 270 MET SELENOMETHIONINE MODRES 3NA6 MSE A 315 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 37 8 HET MSE A 136 16 HET MSE A 174 8 HET MSE A 193 8 HET MSE A 201 8 HET MSE A 215 8 HET MSE A 242 8 HET MSE A 252 8 HET MSE A 270 8 HET MSE A 315 8 HET CL A 331 1 HET CA A 332 1 HET TRS A 333 8 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION HETNAM CA CALCIUM ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 2 CL CL 1- FORMUL 3 CA CA 2+ FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 HOH *313(H2 O) HELIX 1 1 TYR A 62 THR A 75 1 14 HELIX 2 2 ARG A 76 VAL A 80 5 5 HELIX 3 3 ASN A 91 ALA A 97 1 7 HELIX 4 4 ASN A 108 ALA A 112 5 5 HELIX 5 5 THR A 120 THR A 132 1 13 HELIX 6 6 LEU A 133 ALA A 137 5 5 HELIX 7 7 ASP A 163 ASN A 178 1 16 HELIX 8 8 MSE A 193 GLU A 200 1 8 HELIX 9 9 THR A 217 PHE A 235 1 19 SHEET 1 A10 SER A 7 PRO A 8 0 SHEET 2 A10 GLY A 16 PRO A 25 -1 O LYS A 23 N SER A 7 SHEET 3 A10 SER A 35 ASN A 45 -1 O GLN A 44 N GLY A 16 SHEET 4 A10 GLY A 82 VAL A 87 -1 O LEU A 84 N ILE A 43 SHEET 5 A10 THR A 50 THR A 54 1 N LEU A 53 O ILE A 85 SHEET 6 A10 VAL A 139 ASP A 142 1 O VAL A 141 N THR A 54 SHEET 7 A10 VAL A 204 GLU A 209 1 O VAL A 206 N ASP A 142 SHEET 8 A10 PHE A 155 HIS A 159 -1 N ALA A 157 O THR A 207 SHEET 9 A10 TYR A 181 LEU A 185 1 O LEU A 185 N ALA A 158 SHEET 10 A10 VAL A 248 THR A 249 1 O VAL A 248 N SER A 182 SHEET 1 B 4 LEU A 150 PHE A 152 0 SHEET 2 B 4 GLY A 305 HIS A 311 -1 O ARG A 310 N ASP A 151 SHEET 3 B 4 CYS A 321 GLY A 326 -1 O GLY A 326 N VAL A 306 SHEET 4 B 4 LEU A 259 PHE A 260 -1 N LEU A 259 O ALA A 322 SHEET 1 C 3 LEU A 150 PHE A 152 0 SHEET 2 C 3 GLY A 305 HIS A 311 -1 O ARG A 310 N ASP A 151 SHEET 3 C 3 PRO A 276 VAL A 277 -1 N VAL A 277 O GLY A 305 SHEET 1 D 4 VAL A 297 ARG A 300 0 SHEET 2 D 4 LEU A 282 TRP A 287 -1 N VAL A 283 O TYR A 299 SHEET 3 D 4 GLY A 265 ILE A 269 -1 N GLU A 268 O ARG A 285 SHEET 4 D 4 MSE A 315 ILE A 316 -1 O ILE A 316 N GLY A 265 SSBOND 1 CYS A 257 CYS A 321 1555 1555 2.07 LINK C MSE A 1 N LYS A 2 1555 1555 1.34 LINK C VAL A 36 N MSE A 37 1555 1555 1.33 LINK C MSE A 37 N ILE A 38 1555 1555 1.33 LINK C PRO A 135 N AMSE A 136 1555 1555 1.33 LINK C PRO A 135 N BMSE A 136 1555 1555 1.34 LINK C AMSE A 136 N ALA A 137 1555 1555 1.34 LINK C BMSE A 136 N ALA A 137 1555 1555 1.33 LINK C ALA A 173 N MSE A 174 1555 1555 1.33 LINK C MSE A 174 N GLN A 175 1555 1555 1.34 LINK C GLY A 192 N MSE A 193 1555 1555 1.33 LINK C MSE A 193 N TYR A 194 1555 1555 1.33 LINK C GLU A 200 N MSE A 201 1555 1555 1.34 LINK C MSE A 201 N GLY A 202 1555 1555 1.33 LINK C GLY A 214 N MSE A 215 1555 1555 1.33 LINK C MSE A 215 N SER A 216 1555 1555 1.32 LINK C AGLU A 241 N MSE A 242 1555 1555 1.32 LINK C BGLU A 241 N MSE A 242 1555 1555 1.32 LINK C MSE A 242 N GLN A 243 1555 1555 1.33 LINK C ASP A 251 N MSE A 252 1555 1555 1.33 LINK C MSE A 252 N PRO A 253 1555 1555 1.35 LINK C ILE A 269 N MSE A 270 1555 1555 1.33 LINK C MSE A 270 N ILE A 271 1555 1555 1.32 LINK C GLY A 314 N MSE A 315 1555 1555 1.33 LINK C MSE A 315 N ILE A 316 1555 1555 1.34 LINK OG1 THR A 81 CA CA A 332 1555 1555 2.59 LINK O GLY A 236 CA CA A 332 1555 1555 2.37 LINK CA CA A 332 O HOH A 434 1555 1555 2.62 LINK CA CA A 332 O HOH A 565 1555 1555 2.55 LINK CA CA A 332 O HOH A 567 1555 1555 2.53 LINK CA CA A 332 O HOH A 568 1555 1555 2.49 CISPEP 1 PHE A 113 PRO A 114 0 7.31 SITE 1 AC1 5 HIS A 58 ARG A 100 ASN A 108 ASN A 110 SITE 2 AC1 5 ARG A 111 SITE 1 AC2 6 THR A 81 GLY A 236 HOH A 434 HOH A 565 SITE 2 AC2 6 HOH A 567 HOH A 568 SITE 1 AC3 13 GLN A 44 GLY A 46 ALA A 47 GLY A 48 SITE 2 AC3 13 THR A 50 GLY A 82 ARG A 83 HOH A 367 SITE 3 AC3 13 HOH A 459 HOH A 469 HOH A 544 HOH A 580 SITE 4 AC3 13 HOH A 607 CRYST1 99.773 99.773 137.179 90.00 90.00 120.00 P 63 2 2 12 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 0.010023 0.005787 0.000000 0.00000 SCALE2 0.000000 0.011573 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007290 0.00000 HETATM 1 N MSE A 1 53.184 14.584 -2.324 1.00 52.05 N ANISOU 1 N MSE A 1 6912 6651 6212 37 445 7 N HETATM 2 CA MSE A 1 53.085 14.829 -0.833 1.00 53.04 C ANISOU 2 CA MSE A 1 7003 6779 6372 17 428 0 C HETATM 3 C MSE A 1 54.033 13.920 -0.024 1.00 49.90 C ANISOU 3 C MSE A 1 6547 6421 5991 20 429 -18 C HETATM 4 O MSE A 1 54.133 12.727 -0.304 1.00 47.27 O ANISOU 4 O MSE A 1 6204 6104 5651 52 417 -27 O HETATM 5 CB MSE A 1 51.641 14.618 -0.341 1.00 54.08 C ANISOU 5 CB MSE A 1 7150 6882 6515 38 384 0 C HETATM 6 CG MSE A 1 50.841 15.889 -0.080 1.00 61.25 C ANISOU 6 CG MSE A 1 8089 7756 7427 21 378 11 C HETATM 7 SE MSE A 1 49.071 15.456 0.621 0.75 76.11 SE ANISOU 7 SE MSE A 1 9977 9614 9324 49 323 5 SE HETATM 8 CE MSE A 1 48.253 14.703 -0.995 1.00 61.34 C ANISOU 8 CE MSE A 1 8152 7733 7421 93 308 6 C