HEADER ISOMERASE 01-FEB-10 3LMZ TITLE CRYSTAL STRUCTURE OF PUTATIVE SUGAR ISOMERASE. (YP_001305105.1) FROM TITLE 2 PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.44 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE SUGAR ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 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_3797; 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 SUGAR ISOMERASE., STRUCTURAL GENOMICS, JOINT CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, KEYWDS 3 ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 5 01-FEB-23 3LMZ 1 REMARK SEQADV REVDAT 4 17-JUL-19 3LMZ 1 REMARK LINK REVDAT 3 25-OCT-17 3LMZ 1 REMARK REVDAT 2 13-JUL-11 3LMZ 1 VERSN REVDAT 1 23-FEB-10 3LMZ 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE SUGAR ISOMERASE. JRNL TITL 2 (YP_001305105.1) FROM PARABACTEROIDES DISTASONIS ATCC 8503 JRNL TITL 3 AT 1.44 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.5 REMARK 3 NUMBER OF REFLECTIONS : 47252 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) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2401 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) : 1.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.48 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3322 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 186 REMARK 3 BIN FREE R VALUE : 0.3190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2003 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 410 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 17.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.63000 REMARK 3 B22 (A**2) : 0.96000 REMARK 3 B33 (A**2) : -0.33000 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): 0.063 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.072 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2191 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1508 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2971 ; 1.688 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3690 ; 0.979 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 272 ; 5.726 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 96 ;34.271 ;23.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 385 ;12.257 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;14.498 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 317 ; 0.107 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2448 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 442 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 475 ; 0.245 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1574 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1062 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1039 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 265 ; 0.174 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 13 ; 0.270 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 53 ; 0.262 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 34 ; 0.156 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1465 ; 1.763 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 529 ; 0.457 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2156 ; 2.104 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 965 ; 4.069 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 815 ; 5.490 ;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 : 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 33 A 103 REMARK 3 ORIGIN FOR THE GROUP (A): 3.5587 26.9606 39.5202 REMARK 3 T TENSOR REMARK 3 T11: -0.0304 T22: -0.0056 REMARK 3 T33: -0.0059 T12: -0.0085 REMARK 3 T13: -0.0015 T23: -0.0009 REMARK 3 L TENSOR REMARK 3 L11: 0.2581 L22: 0.5870 REMARK 3 L33: 0.5163 L12: 0.1783 REMARK 3 L13: 0.3599 L23: 0.1671 REMARK 3 S TENSOR REMARK 3 S11: 0.0247 S12: -0.0473 S13: -0.0205 REMARK 3 S21: -0.0035 S22: -0.0108 S23: 0.0374 REMARK 3 S31: 0.0412 S32: -0.0497 S33: -0.0139 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 104 A 283 REMARK 3 ORIGIN FOR THE GROUP (A): 18.0798 18.1196 37.2050 REMARK 3 T TENSOR REMARK 3 T11: -0.0124 T22: -0.0119 REMARK 3 T33: -0.0001 T12: 0.0114 REMARK 3 T13: -0.0135 T23: 0.0000 REMARK 3 L TENSOR REMARK 3 L11: 0.4398 L22: 0.0662 REMARK 3 L33: 0.6736 L12: -0.1058 REMARK 3 L13: 0.4515 L23: -0.0606 REMARK 3 S TENSOR REMARK 3 S11: 0.0496 S12: 0.0247 S13: -0.0430 REMARK 3 S21: 0.0032 S22: -0.0045 S23: -0.0266 REMARK 3 S31: 0.0837 S32: 0.0854 S33: -0.0451 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. A REMARK 3 CITRATE (CIT) MOLECULE IS MODELLED FROM CRYSTALLIZATION REMARK 3 CONDITIONS, AND PEG-3000 FRAGMENT FROM CRYSTALLIZATION OR PEG- REMARK 3 400 FRAGMENT FROM CRYO CONDITIONS (PEG AND PGE) ARE MODELED. 5. REMARK 3 THE NOMINAL RESOLUTION IS 1.55 A WITH 9570 OBSERVED REFLECTIONS REMARK 3 BETWEEN 1.55-1.44 A (87.7% COMPLETE FOR THIS SHELL) INCLUDED IN REMARK 3 THE REFINEMENT. REMARK 4 REMARK 4 3LMZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-10. REMARK 100 THE DEPOSITION ID IS D_1000057477. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.57 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) : 0.91162,0.97944,0.97932 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 : 47272 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 28.355 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 76.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49000 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 (%): 52.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19.5000% POLYETHYLENE GLYCOL 3000, REMARK 280 0.1M CITRIC ACID PH 5.57, NANODROP, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 47.74250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.74250 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 39.29700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.95300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.29700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.95300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.74250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.29700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.95300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 47.74250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.29700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.95300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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: STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER REMARK 300 AS A SIGNIFICANT OLIGOMERIZATION STATE. 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: 4440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 47.74250 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 453 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 485 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 ALA A 28 REMARK 465 LEU A 29 REMARK 465 PRO A 30 REMARK 465 ASP A 31 REMARK 465 PRO A 32 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 165 CD CE NZ REMARK 470 LYS A 235 CE NZ 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 ASP A 264 67.08 -156.02 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 CIT A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 396625 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT (RESIDUES 28-283) 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 3LMZ A 28 283 UNP A6LIG9 A6LIG9_PARD8 28 283 SEQADV 3LMZ GLY A 0 UNP A6LIG9 EXPRESSION TAG SEQRES 1 A 257 GLY ALA LEU PRO ASP PRO VAL LYS PRO LYS ALA PRO LYS SEQRES 2 A 257 ALA VAL ASN PRO PHE HIS LEU GLY MSE ALA GLY TYR THR SEQRES 3 A 257 PHE VAL ASN PHE ASP LEU ASP THR THR LEU LYS THR LEU SEQRES 4 A 257 GLU ARG LEU ASP ILE HIS TYR LEU CYS ILE LYS ASP PHE SEQRES 5 A 257 HIS LEU PRO LEU ASN SER THR ASP GLU GLN ILE ARG ALA SEQRES 6 A 257 PHE HIS ASP LYS CYS ALA ALA HIS LYS VAL THR GLY TYR SEQRES 7 A 257 ALA VAL GLY PRO ILE TYR MSE LYS SER GLU GLU GLU ILE SEQRES 8 A 257 ASP ARG ALA PHE ASP TYR ALA LYS ARG VAL GLY VAL LYS SEQRES 9 A 257 LEU ILE VAL GLY VAL PRO ASN TYR GLU LEU LEU PRO TYR SEQRES 10 A 257 VAL ASP LYS LYS VAL LYS GLU TYR ASP PHE HIS TYR ALA SEQRES 11 A 257 ILE HIS LEU HIS GLY PRO ASP ILE LYS THR TYR PRO ASP SEQRES 12 A 257 ALA THR ASP VAL TRP VAL HIS THR LYS ASP LEU ASP PRO SEQRES 13 A 257 ARG ILE GLY MSE CYS LEU ASP VAL GLY HIS ASP LEU ARG SEQRES 14 A 257 ASN GLY CYS ASP PRO VAL ALA ASP LEU LYS LYS TYR HIS SEQRES 15 A 257 THR ARG VAL PHE ASP MSE HIS ILE LYS ASP VAL THR ASP SEQRES 16 A 257 SER SER LYS ALA GLY VAL GLY ILE GLU ILE GLY ARG GLY SEQRES 17 A 257 LYS ILE ASP PHE PRO ALA LEU ILE ARG MSE MSE ARG GLU SEQRES 18 A 257 VAL ASN TYR THR GLY MSE CYS SER LEU GLU TYR GLU LYS SEQRES 19 A 257 ASP MSE LYS ASP PRO PHE LEU GLY ILE ALA GLU SER ILE SEQRES 20 A 257 GLY TYR PHE LYS ALA VAL SER ASP LEU THR MODRES 3LMZ MSE A 48 MET SELENOMETHIONINE MODRES 3LMZ MSE A 111 MET SELENOMETHIONINE MODRES 3LMZ MSE A 186 MET SELENOMETHIONINE MODRES 3LMZ MSE A 214 MET SELENOMETHIONINE MODRES 3LMZ MSE A 244 MET SELENOMETHIONINE MODRES 3LMZ MSE A 245 MET SELENOMETHIONINE MODRES 3LMZ MSE A 253 MET SELENOMETHIONINE MODRES 3LMZ MSE A 262 MET SELENOMETHIONINE HET MSE A 48 16 HET MSE A 111 8 HET MSE A 186 8 HET MSE A 214 8 HET MSE A 244 8 HET MSE A 245 8 HET MSE A 253 16 HET MSE A 262 8 HET CIT A 1 13 HET PEG A 2 7 HET PGE A 3 10 HETNAM MSE SELENOMETHIONINE HETNAM CIT CITRIC ACID HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PGE TRIETHYLENE GLYCOL FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 CIT C6 H8 O7 FORMUL 3 PEG C4 H10 O3 FORMUL 4 PGE C6 H14 O4 FORMUL 5 HOH *410(H2 O) HELIX 1 1 GLY A 50 VAL A 54 5 5 HELIX 2 2 ASP A 57 LEU A 68 1 12 HELIX 3 3 THR A 85 HIS A 99 1 15 HELIX 4 4 SER A 113 GLY A 128 1 16 HELIX 5 5 LEU A 140 ASP A 152 1 13 HELIX 6 6 ASP A 169 LYS A 178 1 10 HELIX 7 7 VAL A 190 ASN A 196 1 7 HELIX 8 8 ASP A 199 HIS A 208 1 10 HELIX 9 9 ASP A 237 VAL A 248 1 12 HELIX 10 10 PRO A 265 THR A 283 1 19 SHEET 1 A 9 HIS A 45 MSE A 48 0 SHEET 2 A 9 TYR A 72 ILE A 75 1 O CYS A 74 N MSE A 48 SHEET 3 A 9 THR A 102 MSE A 111 1 O GLY A 107 N ILE A 75 SHEET 4 A 9 LEU A 131 PRO A 136 1 O VAL A 133 N VAL A 106 SHEET 5 A 9 HIS A 154 HIS A 158 1 O ALA A 156 N ILE A 132 SHEET 6 A 9 ILE A 184 ASP A 189 1 O GLY A 185 N TYR A 155 SHEET 7 A 9 VAL A 211 ILE A 216 1 O ASP A 213 N LEU A 188 SHEET 8 A 9 MSE A 253 LEU A 256 1 O SER A 255 N MSE A 214 SHEET 9 A 9 HIS A 45 MSE A 48 1 N GLY A 47 O CYS A 254 SHEET 1 B 2 ASP A 218 VAL A 219 0 SHEET 2 B 2 GLY A 228 ILE A 229 -1 O ILE A 229 N ASP A 218 LINK C GLY A 47 N AMSE A 48 1555 1555 1.33 LINK C GLY A 47 N BMSE A 48 1555 1555 1.33 LINK C AMSE A 48 N ALA A 49 1555 1555 1.33 LINK C BMSE A 48 N ALA A 49 1555 1555 1.33 LINK C TYR A 110 N MSE A 111 1555 1555 1.32 LINK C MSE A 111 N LYS A 112 1555 1555 1.33 LINK C GLY A 185 N MSE A 186 1555 1555 1.32 LINK C MSE A 186 N CYS A 187 1555 1555 1.35 LINK C ASP A 213 N MSE A 214 1555 1555 1.34 LINK C MSE A 214 N HIS A 215 1555 1555 1.34 LINK C ARG A 243 N MSE A 244 1555 1555 1.33 LINK C MSE A 244 N MSE A 245 1555 1555 1.31 LINK C MSE A 245 N ARG A 246 1555 1555 1.33 LINK C GLY A 252 N AMSE A 253 1555 1555 1.33 LINK C GLY A 252 N BMSE A 253 1555 1555 1.34 LINK C AMSE A 253 N ACYS A 254 1555 1555 1.34 LINK C BMSE A 253 N BCYS A 254 1555 1555 1.34 LINK C ASP A 261 N MSE A 262 1555 1555 1.34 LINK C MSE A 262 N LYS A 263 1555 1555 1.34 CISPEP 1 GLY A 107 PRO A 108 0 1.63 SITE 1 AC1 13 HOH A 6 TYR A 51 LYS A 76 PRO A 108 SITE 2 AC1 13 TYR A 110 HIS A 158 HIS A 160 HIS A 192 SITE 3 AC1 13 LYS A 217 GLU A 257 GLU A 259 HOH A 285 SITE 4 AC1 13 HOH A 370 SITE 1 AC2 7 LYS A 125 GLU A 150 THR A 220 ASP A 221 SITE 2 AC2 7 HOH A 297 HOH A 526 HOH A 575 SITE 1 AC3 5 ASP A 77 ASN A 83 HOH A 589 HOH A 610 SITE 2 AC3 5 HOH A 645 CRYST1 78.594 81.906 95.485 90.00 90.00 90.00 C 2 2 21 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 0.012724 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012209 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010473 0.00000