HEADER HYDROLASE 11-APR-14 4Q34 TITLE CRYSTAL STRUCTURE OF A PUTATIVE ESTERASE (BDI_1566) FROM TITLE 2 PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.60 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 20-341; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARABACTEROIDES DISTASONIS; SOURCE 3 ORGANISM_TAXID: 435591; SOURCE 4 STRAIN: ATCC 8503 / DSM 20701 / NCTC 11152; SOURCE 5 GENE: BDI_1566; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: PB1; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS ALPHA/BETA HYDROLASE FAMILY (PF12697), STRUCTURAL GENOMICS, JOINT KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 PSI-BIOLOGY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 3 01-FEB-23 4Q34 1 REMARK SEQADV LINK REVDAT 2 22-NOV-17 4Q34 1 REMARK REVDAT 1 18-JUN-14 4Q34 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A PUTATIVE ESTERASE (BDI_1566) FROM JRNL TITL 2 PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.60 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 50204 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2562 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3391 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE SET COUNT : 208 REMARK 3 BIN FREE R VALUE : 0.3340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2572 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 322 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.64000 REMARK 3 B22 (A**2) : 1.64000 REMARK 3 B33 (A**2) : -3.29000 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): 0.075 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.298 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.963 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2813 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2625 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3840 ; 1.513 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6057 ; 0.800 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 359 ; 6.023 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 141 ;33.304 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 428 ;13.725 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;17.163 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 406 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3233 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 695 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 21 A 341 REMARK 3 ORIGIN FOR THE GROUP (A): 19.4565 7.2488 90.3092 REMARK 3 T TENSOR REMARK 3 T11: 0.0485 T22: 0.0413 REMARK 3 T33: 0.1110 T12: 0.0086 REMARK 3 T13: -0.0053 T23: -0.0008 REMARK 3 L TENSOR REMARK 3 L11: 0.5226 L22: 0.3273 REMARK 3 L33: 0.8388 L12: -0.0786 REMARK 3 L13: -0.0993 L23: -0.0135 REMARK 3 S TENSOR REMARK 3 S11: 0.0058 S12: 0.0405 S13: -0.0640 REMARK 3 S21: -0.0419 S22: -0.0045 S23: -0.0030 REMARK 3 S31: 0.1090 S32: 0.0240 S33: -0.0013 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.ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B REMARK 3 FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U REMARK 3 FACTORS. 4.WATERS WERE EXCLUDED FROM TLS ASSIGNMENT. 5.CHLORIDE REMARK 3 (CL) FROM THE CRYSTALLIZATION AND GLYCEROL (GOL) USED AS A REMARK 3 CRYOPROTECTANT HAVE BEEN MODELED INTO THE STRUCTURE REMARK 4 REMARK 4 4Q34 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000085543. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JAN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97895,0.97843 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(111) BENT REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING); REMARK 200 SINGLE CRYSTAL SI(111) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE DECEMBER 6, 2010 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50356 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 29.663 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 7.720 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.25300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.330 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHARP, SHELXD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.00M LITHIUM CHLORIDE, 20.00% REMARK 280 POLYETHYLENE GLYCOL 6000, 0.1M CITRIC ACID PH 5.0, NANODROP, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 104.79550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.66350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.66350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 52.39775 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.66350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.66350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 157.19325 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.66350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.66350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 52.39775 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.66350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.66350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 157.19325 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 104.79550 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: 8410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 209.59100 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 521 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 ASP A 20 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 GLU A 21 CG CD OE1 OE2 REMARK 470 ILE A 236 CG1 CG2 CD1 REMARK 470 LYS A 241 CG CD CE NZ REMARK 470 GLU A 273 CD OE1 OE2 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 OD2 ASP A 126 O HOH A 700 2.14 REMARK 500 O HOH A 623 O HOH A 760 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O3 GOL A 407 O HOH A 617 7556 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLU A 81 -149.16 -94.44 REMARK 500 ALA A 112 31.89 -95.52 REMARK 500 SER A 194 -114.29 60.86 REMARK 500 PHE A 317 69.68 -113.19 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 408 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: JCSG-419709 RELATED DB: TARGETTRACK REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT (RESIDUES 20-341) WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 4Q34 A 20 341 UNP A6LCA7 A6LCA7_PARD8 20 341 SEQADV 4Q34 GLY A 0 UNP A6LCA7 EXPRESSION TAG SEQRES 1 A 323 GLY ASP GLU ARG VAL LEU MSE VAL ASP GLU GLN GLY SER SEQRES 2 A 323 PHE ALA VAL GLY GLY THR VAL LEU VAL ASP SER LEU GLY SEQRES 3 A 323 HIS THR PHE HIS GLY ASP HIS ALA TYR VAL PHE TYR GLN SEQRES 4 A 323 LYS PRO VAL GLY ALA ARG LYS TYR PRO LEU VAL PHE ALA SEQRES 5 A 323 HIS GLY VAL GLY GLN PHE SER LYS THR TRP GLU THR THR SEQRES 6 A 323 PRO ASP GLY ARG GLU GLY PHE GLN ASN ILE PHE LEU ARG SEQRES 7 A 323 ARG ARG PHE CYS VAL TYR LEU VAL ASP GLN PRO ARG ARG SEQRES 8 A 323 GLY ASN ALA GLY ARG GLY THR GLU SER VAL THR ILE SER SEQRES 9 A 323 PRO ALA PHE ASP GLU GLU VAL TRP PHE ASN ARG PHE ARG SEQRES 10 A 323 VAL GLY ILE TRP PRO ASP TYR PHE GLU GLY VAL GLN PHE SEQRES 11 A 323 LYS ARG ASP LYS GLU THR LEU ASP GLN TYR PHE ARG GLN SEQRES 12 A 323 MSE THR PRO THR ILE GLY THR THR ASP PHE GLU VAL TYR SEQRES 13 A 323 SER ASP ALA TYR ALA ALA LEU PHE ASP LYS ILE GLY PRO SEQRES 14 A 323 GLY VAL PHE ILE THR HIS SER GLN GLY GLY PRO VAL GLY SEQRES 15 A 323 TRP ASN THR LEU LEU LYS THR ARG ASN ILE LYS ALA ILE SEQRES 16 A 323 ALA SER TYR GLU PRO GLY GLY ALA VAL PRO PHE PRO GLU SEQRES 17 A 323 GLY GLN LEU PRO GLU GLU ALA LYS PHE ILE THR LEU SER SEQRES 18 A 323 LYS LYS MSE GLU GLY ILE GLU VAL PRO MSE SER VAL PHE SEQRES 19 A 323 MSE GLU TYR THR LYS VAL PRO ILE VAL ILE TYR TYR GLY SEQRES 20 A 323 ASP ASN LEU PRO GLU THR ASP GLU ARG PRO GLU LEU TYR SEQRES 21 A 323 GLU TRP THR ARG ARG LEU ARG LEU MSE LYS ILE TRP ALA SEQRES 22 A 323 LYS MSE LEU ASN ASP GLN GLY GLY ASP VAL THR VAL ILE SEQRES 23 A 323 HIS LEU PRO GLU VAL GLY LEU HIS GLY ASN THR HIS PHE SEQRES 24 A 323 PRO MSE SER ASP LEU ASN ASN ILE GLU VAL ALA ASP LEU SEQRES 25 A 323 LEU SER GLU TRP LEU HIS THR LYS ALA LEU ASP MODRES 4Q34 MSE A 25 MET SELENOMETHIONINE MODRES 4Q34 MSE A 162 MET SELENOMETHIONINE MODRES 4Q34 MSE A 242 MET SELENOMETHIONINE MODRES 4Q34 MSE A 249 MET SELENOMETHIONINE MODRES 4Q34 MSE A 253 MET SELENOMETHIONINE MODRES 4Q34 MSE A 287 MET SELENOMETHIONINE MODRES 4Q34 MSE A 293 MET SELENOMETHIONINE MODRES 4Q34 MSE A 319 MET SELENOMETHIONINE HET MSE A 25 13 HET MSE A 162 13 HET MSE A 242 13 HET MSE A 249 8 HET MSE A 253 8 HET MSE A 287 8 HET MSE A 293 8 HET MSE A 319 8 HET CL A 401 1 HET CL A 402 1 HET CL A 403 1 HET GOL A 404 6 HET GOL A 405 6 HET GOL A 406 6 HET GOL A 407 6 HET GOL A 408 6 HETNAM MSE SELENOMETHIONINE HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 CL 3(CL 1-) FORMUL 5 GOL 5(C3 H8 O3) FORMUL 10 HOH *322(H2 O) HELIX 1 1 PHE A 76 GLU A 81 5 6 HELIX 2 2 GLY A 89 ARG A 97 1 9 HELIX 3 3 ARG A 109 GLY A 113 5 5 HELIX 4 4 ASP A 126 PHE A 134 1 9 HELIX 5 5 ASP A 151 GLN A 161 1 11 HELIX 6 6 ASP A 170 GLY A 186 1 17 HELIX 7 7 GLN A 195 LEU A 204 1 10 HELIX 8 8 LEU A 205 THR A 207 5 3 HELIX 9 9 PRO A 230 LYS A 234 5 5 HELIX 10 10 PRO A 248 MSE A 253 1 6 HELIX 11 11 GLU A 254 LYS A 257 5 4 HELIX 12 12 ARG A 274 ASP A 296 1 23 HELIX 13 13 PRO A 307 GLY A 310 5 4 HELIX 14 14 ASN A 323 LYS A 338 1 16 SHEET 1 A 8 VAL A 26 VAL A 34 0 SHEET 2 A 8 ALA A 52 PRO A 59 -1 O LYS A 58 N GLU A 28 SHEET 3 A 8 VAL A 101 ASP A 105 -1 O LEU A 103 N PHE A 55 SHEET 4 A 8 LEU A 67 ALA A 70 1 N LEU A 67 O TYR A 102 SHEET 5 A 8 GLY A 188 HIS A 193 1 O ILE A 191 N VAL A 68 SHEET 6 A 8 ILE A 210 TYR A 216 1 O LYS A 211 N GLY A 188 SHEET 7 A 8 ILE A 260 TYR A 264 1 O VAL A 261 N SER A 215 SHEET 8 A 8 VAL A 301 HIS A 305 1 O ILE A 304 N ILE A 262 SHEET 1 B 2 THR A 37 VAL A 40 0 SHEET 2 B 2 THR A 46 GLY A 49 -1 O PHE A 47 N LEU A 39 SHEET 1 C 2 GLY A 137 ILE A 138 0 SHEET 2 C 2 ASP A 141 TYR A 142 -1 O ASP A 141 N ILE A 138 SHEET 1 D 2 VAL A 222 PRO A 225 0 SHEET 2 D 2 GLY A 244 VAL A 247 1 O ILE A 245 N PHE A 224 LINK C LEU A 24 N MSE A 25 1555 1555 1.33 LINK C MSE A 25 N VAL A 26 1555 1555 1.32 LINK C GLN A 161 N MSE A 162 1555 1555 1.34 LINK C MSE A 162 N THR A 163 1555 1555 1.33 LINK C LYS A 241 N MSE A 242 1555 1555 1.34 LINK C MSE A 242 N GLU A 243 1555 1555 1.34 LINK C PRO A 248 N MSE A 249 1555 1555 1.33 LINK C MSE A 249 N SER A 250 1555 1555 1.33 LINK C PHE A 252 N MSE A 253 1555 1555 1.34 LINK C MSE A 253 N GLU A 254 1555 1555 1.34 LINK C LEU A 286 N MSE A 287 1555 1555 1.33 LINK C MSE A 287 N LYS A 288 1555 1555 1.34 LINK C LYS A 292 N MSE A 293 1555 1555 1.33 LINK C MSE A 293 N LEU A 294 1555 1555 1.33 LINK C PRO A 318 N MSE A 319 1555 1555 1.32 LINK C MSE A 319 N SER A 320 1555 1555 1.35 CISPEP 1 TRP A 139 PRO A 140 0 6.37 SITE 1 AC1 2 ARG A 133 GLN A 195 SITE 1 AC2 2 LYS A 149 ARG A 150 SITE 1 AC3 4 ASN A 132 ARG A 274 HOH A 613 HOH A 631 SITE 1 AC4 6 TYR A 53 PHE A 55 GLU A 81 GLN A 91 SITE 2 AC4 6 LEU A 103 HOH A 514 SITE 1 AC5 4 ASP A 126 VAL A 129 ARG A 133 GLU A 276 SITE 1 AC6 7 LEU A 204 THR A 207 ARG A 208 ASN A 209 SITE 2 AC6 7 ILE A 210 LYS A 257 HOH A 671 SITE 1 AC7 10 GLY A 35 GLY A 36 VAL A 38 ASP A 156 SITE 2 AC7 10 ARG A 160 ASN A 295 HOH A 617 HOH A 670 SITE 3 AC7 10 HOH A 679 HOH A 722 SITE 1 AC8 4 PHE A 32 LYS A 58 TYR A 102 LYS A 184 CRYST1 59.327 59.327 209.591 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 0.016856 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016856 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004771 0.00000