HEADER HYDROLASE 16-OCT-09 3K9T TITLE CRYSTAL STRUCTURE OF PUTATIVE PEPTIDASE (NP_348812.1) FROM CLOSTRIDIUM TITLE 2 ACETOBUTYLICUM AT 2.37 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE PEPTIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN CONTAINING AMINOPEPTIDASE DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CLOSTRIDIUM ACETOBUTYLICUM; SOURCE 3 ORGANISM_TAXID: 1488; SOURCE 4 GENE: CA_C2195; 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 PUTATIVE PEPTIDASE, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL KEYWDS 2 GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, AMINOPEPTIDASE, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3K9T 1 REMARK SEQADV REVDAT 4 17-JUL-19 3K9T 1 REMARK LINK REVDAT 3 25-OCT-17 3K9T 1 REMARK REVDAT 2 13-JUL-11 3K9T 1 VERSN REVDAT 1 10-NOV-09 3K9T 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE PEPTIDASE (NP_348812.1) FROM JRNL TITL 2 CLOSTRIDIUM ACETOBUTYLICUM AT 2.37 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.37 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) : 2.37 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.06 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 31177 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1576 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) : 2.37 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.43 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2153 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3386 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 221 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 38.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.30000 REMARK 3 B22 (A**2) : -1.30000 REMARK 3 B33 (A**2) : 1.95000 REMARK 3 B12 (A**2) : -0.65000 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): 0.201 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.776 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3506 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2373 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4743 ; 1.609 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5784 ; 0.934 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 424 ; 5.670 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 163 ;36.367 ;24.479 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 614 ;15.293 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;20.717 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 518 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3856 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 716 ; 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): 1648 ; 1.654 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 677 ; 0.419 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2673 ; 3.078 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1063 ; 5.741 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1000 ; 7.737 ;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 0 A 434 REMARK 3 ORIGIN FOR THE GROUP (A): 32.2688 1.6738 64.0806 REMARK 3 T TENSOR REMARK 3 T11: 0.0228 T22: 0.0386 REMARK 3 T33: 0.0327 T12: 0.0107 REMARK 3 T13: 0.0125 T23: -0.0118 REMARK 3 L TENSOR REMARK 3 L11: 0.9216 L22: 0.7499 REMARK 3 L33: 0.4114 L12: 0.1874 REMARK 3 L13: -0.0975 L23: -0.0631 REMARK 3 S TENSOR REMARK 3 S11: 0.0209 S12: 0.0462 S13: 0.0311 REMARK 3 S21: 0.0054 S22: 0.0275 S23: -0.1023 REMARK 3 S31: -0.0296 S32: 0.0239 S33: -0.0484 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.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.ZINC (ZN) REMARK 3 HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON ITS REMARK 3 PRESENCE AS A CO-CRYSTALLIZATION COMPOUND AND ANOMALOUS REMARK 3 DIFFERENCE FOURIER MAP. 5.CHLORIDE (CL), IMIDAZOLE (IMD) AND (4R) REMARK 3 -2-METHYLPENTANE-2,4-DIOL (MRD) FROM THE CRYSTALLIZATION REMARK 3 SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 6.THE REMARK 3 RAMACHANDRAN OUTLIER AT RESIDUE PRO190 IS SUPPORTED BY ELECTRON REMARK 3 DENSITY. REMARK 4 REMARK 4 3K9T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055726. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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) : 0.91837,0.97911 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 : 31178 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.370 REMARK 200 RESOLUTION RANGE LOW (A) : 29.062 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.18900 REMARK 200 R SYM (I) : 0.18900 REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.01000 REMARK 200 R SYM FOR SHELL (I) : 1.01700 REMARK 200 FOR SHELL : 0.800 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 (%): 67.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2000M MGCL2, 40.0000% MPD, 0.1M REMARK 280 IMIDAZOLE PH 8.0, ADDITIVE: 0.006M ZINC CHLORIDE, NANODROP', REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 76.89100 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.39304 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 56.12600 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 76.89100 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 44.39304 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 56.12600 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 76.89100 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 44.39304 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 56.12600 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 76.89100 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 44.39304 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 56.12600 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 76.89100 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 44.39304 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 56.12600 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 76.89100 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 44.39304 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 56.12600 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 88.78608 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 112.25200 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 88.78608 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 112.25200 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 88.78608 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 112.25200 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 88.78608 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 112.25200 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 88.78608 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 112.25200 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 88.78608 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 112.25200 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: CRYSTAL PACKING ANALYSIS AND SIZE-EXCLUSION CHROMATOGRAPHY REMARK 300 COUPLED WITH STATIC LIGHT SCATTERING SUPPORT THE ASSIGNMENT OF A REMARK 300 TRIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 48490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -161.0 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 0.00000 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 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 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 ILE A 374 REMARK 465 TYR A 375 REMARK 465 ARG A 376 REMARK 465 MSE A 377 REMARK 465 ILE A 378 REMARK 465 GLY A 379 REMARK 465 GLY A 380 REMARK 465 GLY A 381 REMARK 465 SER A 382 REMARK 465 ASP A 383 REMARK 465 TYR A 384 REMARK 465 PRO A 385 REMARK 465 PHE A 386 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 LYS A 56 CE NZ REMARK 470 LYS A 60 CE NZ REMARK 470 LYS A 81 CD CE NZ REMARK 470 LYS A 89 CE NZ REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 LYS A 144 CD CE NZ REMARK 470 GLU A 147 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 CYS A 149 CB CYS A 149 SG -0.101 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 PHE A 62 -127.25 47.64 REMARK 500 LYS A 84 91.03 -68.72 REMARK 500 SER A 130 67.37 -150.32 REMARK 500 PRO A 190 -127.38 -76.56 REMARK 500 CYS A 193 -62.80 -91.44 REMARK 500 ASN A 196 48.03 -146.44 REMARK 500 THR A 227 -76.58 65.77 REMARK 500 ASN A 237 32.62 -140.75 REMARK 500 PRO A 293 45.37 -78.95 REMARK 500 SER A 296 -158.57 -109.93 REMARK 500 ARG A 315 -114.49 -103.52 REMARK 500 CYS A 365 169.06 64.00 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 435 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 189 NE2 REMARK 620 2 ASP A 195 OD2 100.9 REMARK 620 3 HIS A 324 NE2 115.8 95.7 REMARK 620 4 IMD A 438 N3 110.9 104.1 124.1 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 435 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 436 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 437 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 438 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 440 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 441 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MRD A 442 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 393080 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DNA SEQUENCING REMARK 999 OF THE CLONED CONSTRUCT SHOWS A SERINE AT POSITION 309 INSTEAD OF A REMARK 999 PROLINE. THE SERINE AT POSITION 309 IS SUPPORTED BY THE ELECTRON REMARK 999 DENSITY. DBREF 3K9T A 1 434 UNP Q97H19 Q97H19_CLOAB 1 434 SEQADV 3K9T GLY A 0 UNP Q97H19 EXPRESSION TAG SEQADV 3K9T SER A 309 UNP Q97H19 PRO 309 SEE REMARK 999 SEQRES 1 A 435 GLY MSE GLU GLU ILE ASN LYS TYR ILE GLN ASN SER SER SEQRES 2 A 435 GLU THR GLY GLY GLU ILE TYR ASN LEU ILE GLU GLU LEU SEQRES 3 A 435 PHE PRO ILE CYS ARG SER ILE THR GLY ASN GLY VAL ARG SEQRES 4 A 435 LYS THR MSE ASP ILE ILE ARG LYS HIS ILE PRO LEU GLU SEQRES 5 A 435 ILE HIS GLU VAL LYS SER GLY THR LYS VAL PHE ASP TRP SEQRES 6 A 435 THR VAL PRO LYS GLU TRP ASN ILE LYS ASP ALA TYR VAL SEQRES 7 A 435 ARG ASN SER LYS GLY GLU LYS VAL ILE ASP PHE LYS GLU SEQRES 8 A 435 ASN ASN LEU HIS VAL MSE SER TYR SER VAL PRO VAL HIS SEQRES 9 A 435 LYS THR MSE THR LEU ASP GLU LEU LYS PRO TYR LEU HIS SEQRES 10 A 435 THR ILE PRO GLY ASN LYS ASP ARG ILE PRO TYR LEU THR SEQRES 11 A 435 SER TYR TYR LYS GLU ASN TRP GLY PHE SER LEU THR GLN SEQRES 12 A 435 ASN LYS PHE ASP GLU LEU CYS ASP ASP ASP TYR GLU VAL SEQRES 13 A 435 VAL ILE ASP SER SER LEU GLU ASP GLY SER LEU THR TYR SEQRES 14 A 435 GLY GLU TYR TYR ILE ARG GLY GLU LEU GLU GLU GLU ILE SEQRES 15 A 435 LEU LEU THR THR TYR THR CYS HIS PRO SER MSE CYS ASN SEQRES 16 A 435 ASP ASN LEU SER GLY VAL ALA LEU ILE THR PHE ILE ALA SEQRES 17 A 435 LYS ALA LEU SER LYS LEU LYS THR LYS TYR SER TYR ARG SEQRES 18 A 435 PHE LEU PHE ALA PRO GLU THR ILE GLY SER ILE THR TRP SEQRES 19 A 435 LEU SER ARG ASN GLU ASP LYS LEU LYS ASN ILE LYS MSE SEQRES 20 A 435 GLY LEU VAL ALA THR CYS VAL GLY ASP ALA GLY ILE LYS SEQRES 21 A 435 ASN TYR LYS ARG THR LYS PHE GLY ASP ALA GLU ILE ASP SEQRES 22 A 435 LYS ILE VAL GLU LYS VAL LEU MSE HIS CYS GLY SER GLU SEQRES 23 A 435 TYR TYR VAL ALA ASP PHE PHE PRO TRP GLY SER ASP GLU SEQRES 24 A 435 ARG GLN PHE SER SER PRO GLY ILE ASN LEU SER VAL GLY SEQRES 25 A 435 SER LEU MSE ARG SER CYS TYR GLY PHE ASP GLY TYR HIS SEQRES 26 A 435 THR SER ALA ASP ASN LEU CYS TYR MSE ASN LYS ASP GLY SEQRES 27 A 435 LEU ALA ASP SER TYR LYS THR TYR LEU GLU VAL ILE TYR SEQRES 28 A 435 THR ILE GLU ASN ASN ARG THR TYR LEU ASN LEU ASN PRO SEQRES 29 A 435 LYS CYS GLU PRO GLN LEU GLY LYS ARG GLY ILE TYR ARG SEQRES 30 A 435 MSE ILE GLY GLY GLY SER ASP TYR PRO PHE ASP GLU PHE SEQRES 31 A 435 ALA MSE PHE TRP VAL LEU ASN MSE SER ASP GLY LYS ASN SEQRES 32 A 435 SER LEU LEU ASP ILE ALA TYR LYS SER GLY MSE GLU PHE SEQRES 33 A 435 ARG ARG ILE LYS TYR ALA ALA ASP ALA LEU TYR ARG VAL SEQRES 34 A 435 GLU LEU LEU LYS LEU VAL MODRES 3K9T MSE A 1 MET SELENOMETHIONINE MODRES 3K9T MSE A 41 MET SELENOMETHIONINE MODRES 3K9T MSE A 96 MET SELENOMETHIONINE MODRES 3K9T MSE A 106 MET SELENOMETHIONINE MODRES 3K9T MSE A 192 MET SELENOMETHIONINE MODRES 3K9T MSE A 246 MET SELENOMETHIONINE MODRES 3K9T MSE A 280 MET SELENOMETHIONINE MODRES 3K9T MSE A 314 MET SELENOMETHIONINE MODRES 3K9T MSE A 333 MET SELENOMETHIONINE MODRES 3K9T MSE A 391 MET SELENOMETHIONINE MODRES 3K9T MSE A 397 MET SELENOMETHIONINE MODRES 3K9T MSE A 413 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 41 8 HET MSE A 96 8 HET MSE A 106 8 HET MSE A 192 8 HET MSE A 246 8 HET MSE A 280 8 HET MSE A 314 8 HET MSE A 333 8 HET MSE A 391 8 HET MSE A 397 8 HET MSE A 413 8 HET ZN A 435 1 HET CL A 436 1 HET CL A 437 1 HET IMD A 438 5 HET MRD A 439 8 HET MRD A 440 8 HET MRD A 441 8 HET MRD A 442 8 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM IMD IMIDAZOLE HETNAM MRD (4R)-2-METHYLPENTANE-2,4-DIOL FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 2 ZN ZN 2+ FORMUL 3 CL 2(CL 1-) FORMUL 5 IMD C3 H5 N2 1+ FORMUL 6 MRD 4(C6 H14 O2) FORMUL 10 HOH *221(H2 O) HELIX 1 1 GLY A 0 GLU A 2 5 3 HELIX 2 2 GLU A 3 ASN A 10 1 8 HELIX 3 3 ASN A 10 PHE A 26 1 17 HELIX 4 4 GLY A 34 ARG A 45 1 12 HELIX 5 5 ASN A 91 VAL A 95 5 5 HELIX 6 6 LEU A 108 LYS A 112 1 5 HELIX 7 7 THR A 141 GLU A 147 1 7 HELIX 8 8 ASN A 196 SER A 211 1 16 HELIX 9 9 THR A 227 ASN A 237 1 11 HELIX 10 10 GLU A 238 LYS A 242 5 5 HELIX 11 11 ALA A 269 CYS A 282 1 14 HELIX 12 12 ASP A 297 SER A 302 1 6 HELIX 13 13 ASN A 329 MSE A 333 5 5 HELIX 14 14 ASN A 334 ASN A 355 1 22 HELIX 15 15 ASP A 387 SER A 398 1 12 HELIX 16 16 LEU A 404 GLY A 412 1 9 HELIX 17 17 GLU A 414 VAL A 428 1 15 SHEET 1 A 8 GLU A 51 LYS A 56 0 SHEET 2 A 8 SER A 165 ILE A 173 -1 O TYR A 168 N HIS A 53 SHEET 3 A 8 SER A 218 ALA A 224 -1 O PHE A 223 N GLY A 169 SHEET 4 A 8 GLU A 180 TYR A 186 1 N LEU A 183 O ARG A 220 SHEET 5 A 8 ILE A 244 VAL A 249 1 O LYS A 245 N GLU A 180 SHEET 6 A 8 VAL A 310 MSE A 314 1 O GLY A 311 N VAL A 249 SHEET 7 A 8 LYS A 259 LYS A 262 -1 N ASN A 260 O MSE A 314 SHEET 8 A 8 TYR A 286 ALA A 289 1 O ALA A 289 N TYR A 261 SHEET 1 B 2 LYS A 60 VAL A 61 0 SHEET 2 B 2 TRP A 64 THR A 65 -1 O TRP A 64 N VAL A 61 SHEET 1 C 4 LYS A 84 ASP A 87 0 SHEET 2 C 4 GLU A 69 ARG A 78 -1 N VAL A 77 O ILE A 86 SHEET 3 C 4 ASP A 152 GLU A 162 -1 O GLU A 154 N ARG A 78 SHEET 4 C 4 VAL A 102 THR A 107 -1 N MSE A 106 O TYR A 153 SHEET 1 D 2 LEU A 115 HIS A 116 0 SHEET 2 D 2 PHE A 138 SER A 139 1 O PHE A 138 N HIS A 116 SHEET 1 E 3 ASP A 399 SER A 403 0 SHEET 2 E 3 THR A 357 ASN A 360 -1 N TYR A 358 O GLY A 400 SHEET 3 E 3 LEU A 431 LEU A 433 -1 O LYS A 432 N LEU A 359 SSBOND 1 CYS A 331 CYS A 331 1555 5556 2.04 LINK C GLY A 0 N MSE A 1 1555 1555 1.35 LINK C MSE A 1 N GLU A 2 1555 1555 1.34 LINK C THR A 40 N MSE A 41 1555 1555 1.33 LINK C MSE A 41 N ASP A 42 1555 1555 1.33 LINK C VAL A 95 N MSE A 96 1555 1555 1.33 LINK C MSE A 96 N SER A 97 1555 1555 1.33 LINK C THR A 105 N MSE A 106 1555 1555 1.32 LINK C MSE A 106 N THR A 107 1555 1555 1.33 LINK C SER A 191 N MSE A 192 1555 1555 1.33 LINK C MSE A 192 N CYS A 193 1555 1555 1.33 LINK C LYS A 245 N MSE A 246 1555 1555 1.32 LINK C MSE A 246 N GLY A 247 1555 1555 1.32 LINK C LEU A 279 N MSE A 280 1555 1555 1.33 LINK C MSE A 280 N HIS A 281 1555 1555 1.32 LINK C LEU A 313 N MSE A 314 1555 1555 1.33 LINK C MSE A 314 N ARG A 315 1555 1555 1.33 LINK C TYR A 332 N MSE A 333 1555 1555 1.33 LINK C MSE A 333 N ASN A 334 1555 1555 1.32 LINK C ALA A 390 N MSE A 391 1555 1555 1.32 LINK C MSE A 391 N PHE A 392 1555 1555 1.34 LINK C ASN A 396 N MSE A 397 1555 1555 1.32 LINK C MSE A 397 N SER A 398 1555 1555 1.33 LINK C GLY A 412 N MSE A 413 1555 1555 1.33 LINK C MSE A 413 N GLU A 414 1555 1555 1.32 LINK NE2 HIS A 189 ZN ZN A 435 1555 1555 2.05 LINK OD2 ASP A 195 ZN ZN A 435 1555 1555 1.94 LINK NE2 HIS A 324 ZN ZN A 435 1555 1555 2.06 LINK ZN ZN A 435 N3 IMD A 438 1555 1555 2.04 CISPEP 1 ASP A 195 ASN A 196 0 2.43 SITE 1 AC1 4 HIS A 189 ASP A 195 HIS A 324 IMD A 438 SITE 1 AC2 3 MSE A 413 GLU A 414 ARG A 417 SITE 1 AC3 1 TYR A 172 SITE 1 AC4 7 TYR A 186 HIS A 189 ASP A 195 GLU A 226 SITE 2 AC4 7 GLY A 295 HIS A 324 ZN A 435 SITE 1 AC5 8 TYR A 19 ASN A 329 LEU A 330 CYS A 331 SITE 2 AC5 8 MSE A 333 LYS A 335 MRD A 442 HOH A 504 SITE 1 AC6 5 HIS A 47 TYR A 171 LYS A 208 SER A 211 SITE 2 AC6 5 LYS A 212 SITE 1 AC7 3 TYR A 19 LEU A 330 MRD A 440 CRYST1 153.782 153.782 168.378 90.00 90.00 120.00 H 3 2 18 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 0.006503 0.003754 0.000000 0.00000 SCALE2 0.000000 0.007509 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005939 0.00000