HEADER HYDROLASE 06-NOV-09 3KL7 TITLE CRYSTAL STRUCTURE OF PUTATIVE METAL-DEPENDENT HYDROLASE TITLE 2 (YP_001302908.1) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 2.30 A TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE METAL-DEPENDENT HYDROLASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 26-241; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARABACTEROIDES DISTASONIS ATCC 8503; SOURCE 3 ORGANISM_TAXID: 435591; SOURCE 4 STRAIN: ATCC 8503 / DSM 20701 / NCTC 11152; SOURCE 5 GENE: BDI_1531; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS PUTATIVE METAL-DEPENDENT HYDROLASE, STRUCTURAL GENOMICS, JOINT CENTER KEYWDS 2 FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, KEYWDS 3 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 4 17-JUL-19 3KL7 1 REMARK LINK REVDAT 3 01-NOV-17 3KL7 1 REMARK REVDAT 2 13-JUL-11 3KL7 1 VERSN REVDAT 1 02-FEB-10 3KL7 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE METAL-DEPENDENT HYDROLASE JRNL TITL 2 (YP_001302908.1) FROM PARABACTEROIDES DISTASONIS ATCC 8503 JRNL TITL 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 5.5.0053 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 14894 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 750 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) : 1019 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1734 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 155 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 32.53 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.90000 REMARK 3 B22 (A**2) : 1.90000 REMARK 3 B33 (A**2) : -2.85000 REMARK 3 B12 (A**2) : 0.95000 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): 0.212 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.177 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.122 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.040 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1817 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1241 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2456 ; 1.059 ; 1.978 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3047 ; 0.709 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 225 ; 6.042 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;37.986 ;24.819 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 319 ;12.920 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;12.167 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 270 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1998 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 342 ; 0.000 ; 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): 1109 ; 0.461 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 445 ; 0.090 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1801 ; 0.876 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 708 ; 1.315 ; 4.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 652 ; 1.963 ; 5.000 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 : 2 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 -3 A 46 REMARK 3 ORIGIN FOR THE GROUP (A): 58.2060 17.4790 9.2550 REMARK 3 T TENSOR REMARK 3 T11: 0.1461 T22: 0.0412 REMARK 3 T33: 0.0822 T12: 0.0081 REMARK 3 T13: 0.0115 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 8.6980 L22: 1.8345 REMARK 3 L33: 3.5592 L12: 2.1694 REMARK 3 L13: 0.5973 L23: -0.1679 REMARK 3 S TENSOR REMARK 3 S11: -0.0265 S12: -0.2704 S13: -0.4824 REMARK 3 S21: 0.0526 S22: 0.0310 S23: -0.0487 REMARK 3 S31: 0.4123 S32: -0.0563 S33: -0.0045 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 47 A 241 REMARK 3 ORIGIN FOR THE GROUP (A): 64.3270 28.7200 5.7080 REMARK 3 T TENSOR REMARK 3 T11: 0.0041 T22: 0.0314 REMARK 3 T33: 0.0537 T12: -0.0016 REMARK 3 T13: 0.0060 T23: 0.0111 REMARK 3 L TENSOR REMARK 3 L11: 1.6146 L22: 1.3936 REMARK 3 L33: 2.7523 L12: 0.2356 REMARK 3 L13: 0.3774 L23: 0.1298 REMARK 3 S TENSOR REMARK 3 S11: -0.0257 S12: 0.1146 S13: 0.0344 REMARK 3 S21: 0.0043 S22: 0.0055 S23: -0.0701 REMARK 3 S31: 0.0429 S32: 0.0994 S33: 0.0202 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 TO ACCOUNT FOR THE REMARK 3 REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. REMARK 3 TWO ZINC IONS HAVE BEEN MODELED AT THE PUTATIVE ACTIVE SITE REMARK 3 BASED ON AN X-RAY FLUORESCENCE EXCITATION SCAN SPECTRUM AND REMARK 3 ANOMALOUS DIFFERENCE FOURIER PEAKS. 5. AN UNIDENTIFIED LIGAND REMARK 3 (UNL) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE COORDINATING REMARK 3 THE ZINC SITES. 6. ACETATE (ACT) AND GLYCEROL (GOL) FROM THE REMARK 3 CRYSTALLIZATION/ CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO REMARK 3 THE SOLVENT STRUCTURE. 7. TLS GROUPS WERE ASSIGNED WITH THE AID REMARK 3 OF THE TLSMD SERVER. REMARK 4 REMARK 4 3KL7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056130. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 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) : 0.97920 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 : 14896 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 29.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.22000 REMARK 200 R SYM (I) : 0.22000 REMARK 200 FOR THE DATA SET : 10.2000 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.01300 REMARK 200 R SYM FOR SHELL (I) : 1.25200 REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 59.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 38.0000% POLYETHYLENE GLYCOL 300, REMARK 280 0.2500M CALCIUM ACETATE, 0.1M SODIUM CACODYLATE PH 7.0, NANODROP, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 42.19667 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 21.09833 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 21.09833 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 42.19667 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MSE A -18 REMARK 465 GLY A -17 REMARK 465 SER A -16 REMARK 465 ASP A -15 REMARK 465 LYS A -14 REMARK 465 ILE A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 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 TYR A -3 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 34 NZ REMARK 470 LYS A 88 CD CE NZ REMARK 470 LYS A 117 CD CE NZ REMARK 470 LYS A 229 CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 51 O HOH A 669 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 HIS A 43 -119.20 53.71 REMARK 500 HIS A 84 -43.31 -140.97 REMARK 500 HIS A 149 -33.16 79.22 REMARK 500 THR A 193 -123.60 -128.41 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 302 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 79 NE2 REMARK 620 2 HIS A 81 ND1 92.6 REMARK 620 3 HIS A 146 NE2 98.1 91.9 REMARK 620 4 ASP A 168 OD2 85.7 173.5 94.5 REMARK 620 5 UNL A 301 O1 171.0 95.3 86.0 86.0 REMARK 620 6 HOH A 679 O 103.8 92.2 157.5 82.1 71.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 83 OD2 REMARK 620 2 HIS A 84 NE2 90.6 REMARK 620 3 ASP A 168 OD2 171.7 86.8 REMARK 620 4 HIS A 215 NE2 86.5 93.8 101.5 REMARK 620 5 UNL A 301 O3 86.6 176.0 96.4 83.1 REMARK 620 6 HOH A 679 O 86.2 101.1 86.6 163.4 81.6 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 ZN A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 308 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 393086 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT (26-241) WAS EXPRESSED WITH THE N-TERMINAL REMARK 999 PURIFICATION TAG MGSDKIHHHHHHENLYFQG. DBREF 3KL7 A 26 241 UNP A6LC72 A6LC72_PARD8 26 241 SEQADV 3KL7 MSE A -18 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 GLY A -17 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 SER A -16 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 ASP A -15 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 LYS A -14 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 ILE A -13 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 HIS A -12 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 HIS A -11 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 HIS A -10 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 HIS A -9 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 HIS A -8 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 HIS A -7 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 GLU A -6 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 ASN A -5 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 LEU A -4 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 TYR A -3 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 PHE A -2 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 GLN A -1 UNP A6LC72 EXPRESSION TAG SEQADV 3KL7 GLY A 0 UNP A6LC72 EXPRESSION TAG SEQRES 1 A 235 MSE GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS GLU SEQRES 2 A 235 ASN LEU TYR PHE GLN GLY ASP SER PHE LYS THR LYS SER SEQRES 3 A 235 GLY LYS GLU LEU THR ILE THR PHE ILE LYS HIS GLY SER SEQRES 4 A 235 LEU MSE LEU THR TYR ASP ASN HIS SER ILE GLN VAL ASP SEQRES 5 A 235 PRO VAL SER GLU TYR ALA ASP TYR THR THR PHE PRO LYS SEQRES 6 A 235 ALA ASP ILE ILE LEU ILE THR HIS GLU HIS GLY ASP HIS SEQRES 7 A 235 LEU ASP PRO LYS ALA ILE GLN ALA VAL GLU LYS SER ASP SEQRES 8 A 235 THR GLU ILE ILE ALA ASN GLU ASN SER GLN LYS LYS LEU SEQRES 9 A 235 GLY LYS GLY LYS VAL LEU LYS ASN GLY ASP THR ASP THR SEQRES 10 A 235 SER ILE SER TYR MSE LYS ILE GLU ALA VAL PRO ALA TYR SEQRES 11 A 235 ASN THR THR PRO GLY ARG ASP LYS TYR HIS PRO ARG HIS SEQRES 12 A 235 ARG ASP ASN GLY TYR ILE LEU THR PHE ASP GLY LEU ARG SEQRES 13 A 235 VAL TYR ILE ALA GLY ASP THR GLU ASP ILE PRO GLU MSE SEQRES 14 A 235 LYS ASP LEU LYS ASP ILE ASP ILE ALA PHE LEU PRO VAL SEQRES 15 A 235 ASN GLN PRO TYR THR MSE THR VAL SER GLN ALA ALA LYS SEQRES 16 A 235 ALA ALA ARG MSE PHE SER PRO LYS ILE LEU TYR PRO TYR SEQRES 17 A 235 HIS TYR GLY ASP THR LYS ILE GLY GLU LEU LYS ASP ALA SEQRES 18 A 235 LEU LYS ASP SER GLY ILE ASP VAL ARG ILE ARG GLU LEU SEQRES 19 A 235 GLN MODRES 3KL7 MSE A 47 MET SELENOMETHIONINE MODRES 3KL7 MSE A 128 MET SELENOMETHIONINE MODRES 3KL7 MSE A 175 MET SELENOMETHIONINE MODRES 3KL7 MSE A 194 MET SELENOMETHIONINE MODRES 3KL7 MSE A 205 MET SELENOMETHIONINE HET MSE A 47 8 HET MSE A 128 8 HET MSE A 175 8 HET MSE A 194 8 HET MSE A 205 8 HET UNL A 301 6 HET ZN A 302 1 HET ZN A 303 1 HET ACT A 304 4 HET GOL A 305 6 HET GOL A 306 6 HET GOL A 307 6 HET GOL A 308 6 HETNAM MSE SELENOMETHIONINE HETNAM UNL UNKNOWN LIGAND HETNAM ZN ZINC ION HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 3 ZN 2(ZN 2+) FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 GOL 4(C3 H8 O3) FORMUL 10 HOH *155(H2 O) HELIX 1 1 ASP A 86 GLU A 94 1 9 HELIX 2 2 ASN A 103 GLY A 111 1 9 HELIX 3 3 GLY A 141 TYR A 145 5 5 HELIX 4 4 ILE A 172 LEU A 178 5 7 HELIX 5 5 THR A 195 SER A 207 1 13 HELIX 6 6 GLY A 222 LEU A 228 1 7 SHEET 1 A 7 GLY A 0 LYS A 29 0 SHEET 2 A 7 GLU A 35 LYS A 42 -1 O LEU A 36 N PHE A 28 SHEET 3 A 7 SER A 45 TYR A 50 -1 O MSE A 47 N THR A 39 SHEET 4 A 7 HIS A 53 VAL A 57 -1 O ILE A 55 N LEU A 48 SHEET 5 A 7 ILE A 74 ILE A 77 1 O LEU A 76 N GLN A 56 SHEET 6 A 7 GLU A 99 ALA A 102 1 O ILE A 101 N ILE A 75 SHEET 7 A 7 LYS A 114 VAL A 115 1 O LYS A 114 N ILE A 100 SHEET 1 B 7 THR A 121 ASP A 122 0 SHEET 2 B 7 LYS A 129 PRO A 134 -1 O ILE A 130 N ASP A 122 SHEET 3 B 7 ASN A 152 PHE A 158 -1 O GLY A 153 N VAL A 133 SHEET 4 B 7 LEU A 161 ILE A 165 -1 O ILE A 165 N TYR A 154 SHEET 5 B 7 ILE A 183 PRO A 187 1 O ILE A 183 N TYR A 164 SHEET 6 B 7 ILE A 210 TYR A 214 1 O TYR A 212 N ALA A 184 SHEET 7 B 7 ASP A 234 VAL A 235 1 O ASP A 234 N LEU A 211 LINK C LEU A 46 N MSE A 47 1555 1555 1.33 LINK C MSE A 47 N LEU A 48 1555 1555 1.32 LINK NE2 HIS A 79 ZN ZN A 302 1555 1555 2.29 LINK ND1 HIS A 81 ZN ZN A 302 1555 1555 2.34 LINK OD2 ASP A 83 ZN ZN A 303 1555 1555 2.46 LINK NE2 HIS A 84 ZN ZN A 303 1555 1555 2.27 LINK C TYR A 127 N MSE A 128 1555 1555 1.33 LINK C MSE A 128 N LYS A 129 1555 1555 1.34 LINK NE2 HIS A 146 ZN ZN A 302 1555 1555 2.13 LINK OD2 ASP A 168 ZN ZN A 302 1555 1555 2.30 LINK OD2 ASP A 168 ZN ZN A 303 1555 1555 2.09 LINK C GLU A 174 N MSE A 175 1555 1555 1.31 LINK C MSE A 175 N LYS A 176 1555 1555 1.34 LINK C THR A 193 N MSE A 194 1555 1555 1.33 LINK C MSE A 194 N THR A 195 1555 1555 1.34 LINK C ARG A 204 N MSE A 205 1555 1555 1.32 LINK C MSE A 205 N PHE A 206 1555 1555 1.34 LINK NE2 HIS A 215 ZN ZN A 303 1555 1555 2.16 LINK O1 UNL A 301 ZN ZN A 302 1555 1555 2.41 LINK O3 UNL A 301 ZN ZN A 303 1555 1555 2.60 LINK ZN ZN A 302 O HOH A 679 1555 1555 2.04 LINK ZN ZN A 303 O HOH A 679 1555 1555 2.07 CISPEP 1 GLN A 190 PRO A 191 0 2.40 SITE 1 AC1 6 HIS A 79 HIS A 81 HIS A 146 ASP A 168 SITE 2 AC1 6 ZN A 303 HOH A 679 SITE 1 AC2 6 ASP A 83 HIS A 84 ASP A 168 HIS A 215 SITE 2 AC2 6 ZN A 302 HOH A 679 SITE 1 AC3 5 ASP A 218 THR A 219 GOL A 308 HOH A 547 SITE 2 AC3 5 HOH A 552 SITE 1 AC4 9 GLU A 131 ILE A 155 ARG A 162 ASP A 177 SITE 2 AC4 9 LYS A 179 ASP A 234 ARG A 236 GOL A 307 SITE 3 AC4 9 HOH A 610 SITE 1 AC5 9 TYR A 50 SER A 126 TYR A 127 LYS A 129 SITE 2 AC5 9 THR A 157 ASP A 159 HOH A 551 HOH A 559 SITE 3 AC5 9 HOH A 601 SITE 1 AC6 5 LYS A 129 ARG A 162 ASP A 180 ASP A 234 SITE 2 AC6 5 GOL A 305 SITE 1 AC7 9 VAL A 188 ASN A 189 GLN A 190 MSE A 194 SITE 2 AC7 9 THR A 195 VAL A 196 THR A 219 ACT A 304 SITE 3 AC7 9 HOH A 656 CRYST1 95.034 95.034 63.295 90.00 90.00 120.00 P 32 2 1 6 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 0.010523 0.006075 0.000000 0.00000 SCALE2 0.000000 0.012150 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015799 0.00000