HEADER ISOMERASE 14-DEC-09 3L23 TITLE CRYSTAL STRUCTURE OF SUGAR PHOSPHATE ISOMERASE/EPIMERASE TITLE 2 (YP_001303399.1) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 1.70 A TITLE 3 RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUGAR PHOSPHATE ISOMERASE/EPIMERASE; 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_2046; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS SUGAR PHOSPHATE ISOMERASE/EPIMERASE, STRUCTURAL GENOMICS, JOINT KEYWDS 2 CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, KEYWDS 3 PSI-2, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 4 17-JUL-19 3L23 1 REMARK LINK REVDAT 3 25-OCT-17 3L23 1 REMARK REVDAT 2 13-JUL-11 3L23 1 VERSN REVDAT 1 16-FEB-10 3L23 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF SUGAR PHOSPHATE ISOMERASE/EPIMERASE JRNL TITL 2 (YP_001303399.1) FROM PARABACTEROIDES DISTASONIS ATCC 8503 JRNL TITL 3 AT 1.70 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 36149 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) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1806 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.75 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2428 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.13 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 131 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2185 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 21 REMARK 3 SOLVENT ATOMS : 270 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 19.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : 1.51000 REMARK 3 B33 (A**2) : -1.39000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.22000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.084 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.079 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.520 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.968 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2350 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1587 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3173 ; 1.557 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3898 ; 1.020 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 302 ; 5.299 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;36.251 ;25.294 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 417 ;12.562 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;12.353 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 336 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2658 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 458 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 467 ; 0.211 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1623 ; 0.175 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1153 ; 0.183 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 1117 ; 0.088 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 346 ; 0.187 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.003 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 2 ; 0.139 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 34 ; 0.218 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.257 ; 0.500 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): 1596 ; 1.031 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 594 ; 0.255 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2358 ; 1.385 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 983 ; 2.375 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 814 ; 3.062 ; 4.500 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 43 A 334 REMARK 3 ORIGIN FOR THE GROUP (A): 6.0051 4.6327 17.6303 REMARK 3 T TENSOR REMARK 3 T11: -0.1981 T22: -0.1841 REMARK 3 T33: -0.1716 T12: 0.0051 REMARK 3 T13: -0.0070 T23: 0.0010 REMARK 3 L TENSOR REMARK 3 L11: 1.7138 L22: 1.4560 REMARK 3 L33: 1.5884 L12: 1.0473 REMARK 3 L13: -0.1504 L23: 0.1619 REMARK 3 S TENSOR REMARK 3 S11: 0.0531 S12: -0.1306 S13: 0.0868 REMARK 3 S21: 0.0711 S22: -0.0815 S23: 0.0172 REMARK 3 S31: -0.0388 S32: 0.0724 S33: 0.0284 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.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. REMARK 3 4.MAGNESIUM ION FROM CRYSTALLIZATION AND ETHYLENE GLYCOL REMARK 3 MOLECULES FROM CRYOPROTECTANT ARE MODELED IN THE STRUCTURE, REMARK 3 RESPECTIVELY. REMARK 4 REMARK 4 3L23 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056735. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JUL-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.7 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) : 0.91837,0.97935 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL SI(111) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING) 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 : 36149 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 28.318 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 2.810 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.33900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.970 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 (%): 48.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2000M MGACETATE, 20.0000% PEG-3350, REMARK 280 NO BUFFER PH 7.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 38.82850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.31700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 38.82850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.31700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE REMARK 300 ASSIGNMENT OF A MONOMER 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: MONOMERIC 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 GLY A 0 REMARK 465 ALA A 33 REMARK 465 LEU A 34 REMARK 465 GLY A 35 REMARK 465 VAL A 36 REMARK 465 VAL A 37 REMARK 465 ASP A 38 REMARK 465 GLU A 39 REMARK 465 VAL A 40 REMARK 465 HIS A 41 REMARK 465 ALA A 42 REMARK 465 GLU A 212 REMARK 465 LYS A 213 REMARK 465 VAL A 214 REMARK 465 LYS A 215 REMARK 465 GLY A 216 REMARK 465 ASN A 217 REMARK 465 PRO A 218 REMARK 465 PHE A 219 REMARK 465 ALA A 220 REMARK 465 ALA A 221 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 59 CD CE NZ REMARK 470 LYS A 105 CD CE NZ REMARK 470 SER A 119 OG REMARK 470 PHE A 122 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 123 CG CD CE NZ REMARK 470 LYS A 128 CD CE NZ REMARK 470 GLU A 132 CD OE1 OE2 REMARK 470 LYS A 136 CE NZ REMARK 470 LYS A 150 CD CE NZ REMARK 470 LYS A 208 CG CD CE NZ REMARK 470 GLU A 209 CG CD OE1 OE2 REMARK 470 GLN A 211 CG CD OE1 NE2 REMARK 470 PHE A 222 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 224 CE NZ REMARK 470 LYS A 264 CD CE NZ REMARK 470 LYS A 301 CG CD CE NZ REMARK 470 LYS A 329 CE NZ 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 153 CB CYS A 153 SG -0.139 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 SER A 54 -144.16 53.65 REMARK 500 HIS A 198 -137.29 -107.18 REMARK 500 ALA A 278 -121.36 -148.04 REMARK 500 ALA A 278 -121.36 -141.48 REMARK 500 MSE A 286 119.22 81.82 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 MG A 1 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 247 OD2 REMARK 620 2 GLU A 306 OE1 95.3 REMARK 620 3 HOH A 14 O 87.2 90.1 REMARK 620 4 HOH A 15 O 165.8 84.7 78.6 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 MG A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 4 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 5 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 396634 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED REMARK 999 CONSTRUCT CONTAINS RESIDUES 33-334 OF THE FULL LENGTH PROTEIN. DBREF 3L23 A 33 334 UNP A6LDL3 A6LDL3_PARD8 33 334 SEQADV 3L23 GLY A 0 UNP A6LDL3 LEADER SEQUENCE SEQRES 1 A 303 GLY ALA LEU GLY VAL VAL ASP GLU VAL HIS ALA GLY LYS SEQRES 2 A 303 GLU ILE GLY LEU GLN ILE TYR SER LEU SER GLN GLU LEU SEQRES 3 A 303 TYR LYS GLY ASP VAL ALA ALA ASN LEU ARG LYS VAL LYS SEQRES 4 A 303 ASP MSE GLY TYR SER LYS LEU GLU LEU ALA GLY TYR GLY SEQRES 5 A 303 LYS GLY ALA ILE GLY GLY VAL PRO MSE MSE ASP PHE LYS SEQRES 6 A 303 LYS MSE ALA GLU ASP ALA GLY LEU LYS ILE ILE SER SER SEQRES 7 A 303 HIS VAL ASN PRO VAL ASP THR SER ILE SER ASP PRO PHE SEQRES 8 A 303 LYS ALA MSE ILE PHE LYS TYR SER LYS GLU VAL THR PRO SEQRES 9 A 303 LYS ILE MSE GLU TYR TRP LYS ALA THR ALA ALA ASP HIS SEQRES 10 A 303 ALA LYS LEU GLY CYS LYS TYR LEU ILE GLN PRO MSE MSE SEQRES 11 A 303 PRO THR ILE THR THR HIS ASP GLU ALA LYS LEU VAL CYS SEQRES 12 A 303 ASP ILE PHE ASN GLN ALA SER ASP VAL ILE LYS ALA GLU SEQRES 13 A 303 GLY ILE ALA THR GLY PHE GLY TYR HIS ASN HIS ASN MSE SEQRES 14 A 303 GLU PHE ASN ARG VAL ALA THR LYS GLU GLN GLN GLU LYS SEQRES 15 A 303 VAL LYS GLY ASN PRO PHE ALA ALA PHE MSE LYS VAL GLY SEQRES 16 A 303 ASP GLN ILE TYR ASP LEU MSE LEU LYS ASP THR ASP PRO SEQRES 17 A 303 SER LYS VAL TYR PHE GLU MSE ASP VAL TYR TRP THR VAL SEQRES 18 A 303 MSE GLY GLN ASN ASP PRO VAL GLU TYR MSE GLN LYS HIS SEQRES 19 A 303 PRO ASP ARG ILE LYS VAL LEU HIS ILE LYS ASP ARG ALA SEQRES 20 A 303 VAL PHE GLY GLN SER GLY MSE MSE ASN PHE GLU MSE ILE SEQRES 21 A 303 PHE LYS GLN MSE TYR ALA ASN GLY ILE LYS ASP TYR PHE SEQRES 22 A 303 VAL GLU LEU GLU GLN MSE PRO ASP GLY ARG THR GLN PHE SEQRES 23 A 303 ALA GLY VAL LYS ASP CYS ALA ASP TYR LEU ILE LYS ALA SEQRES 24 A 303 PRO PHE VAL LYS MODRES 3L23 MSE A 72 MET SELENOMETHIONINE MODRES 3L23 MSE A 92 MET SELENOMETHIONINE MODRES 3L23 MSE A 93 MET SELENOMETHIONINE MODRES 3L23 MSE A 98 MET SELENOMETHIONINE MODRES 3L23 MSE A 125 MET SELENOMETHIONINE MODRES 3L23 MSE A 138 MET SELENOMETHIONINE MODRES 3L23 MSE A 160 MET SELENOMETHIONINE MODRES 3L23 MSE A 161 MET SELENOMETHIONINE MODRES 3L23 MSE A 200 MET SELENOMETHIONINE MODRES 3L23 MSE A 223 MET SELENOMETHIONINE MODRES 3L23 MSE A 233 MET SELENOMETHIONINE MODRES 3L23 MSE A 246 MET SELENOMETHIONINE MODRES 3L23 MSE A 253 MET SELENOMETHIONINE MODRES 3L23 MSE A 262 MET SELENOMETHIONINE MODRES 3L23 MSE A 285 MET SELENOMETHIONINE MODRES 3L23 MSE A 286 MET SELENOMETHIONINE MODRES 3L23 MSE A 290 MET SELENOMETHIONINE MODRES 3L23 MSE A 295 MET SELENOMETHIONINE MODRES 3L23 MSE A 310 MET SELENOMETHIONINE HET MSE A 72 8 HET MSE A 92 8 HET MSE A 93 8 HET MSE A 98 8 HET MSE A 125 16 HET MSE A 138 8 HET MSE A 160 8 HET MSE A 161 8 HET MSE A 200 8 HET MSE A 223 8 HET MSE A 233 8 HET MSE A 246 8 HET MSE A 253 8 HET MSE A 262 16 HET MSE A 285 13 HET MSE A 286 8 HET MSE A 290 8 HET MSE A 295 8 HET MSE A 310 8 HET MG A 1 1 HET EDO A 2 4 HET EDO A 3 4 HET EDO A 4 4 HET EDO A 5 4 HET EDO A 6 4 HETNAM MSE SELENOMETHIONINE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 19(C5 H11 N O2 SE) FORMUL 2 MG MG 2+ FORMUL 3 EDO 5(C2 H6 O2) FORMUL 8 HOH *270(H2 O) HELIX 1 1 TYR A 51 LYS A 59 5 9 HELIX 2 2 ASP A 61 MSE A 72 1 12 HELIX 3 3 MSE A 92 ALA A 102 1 11 HELIX 4 4 VAL A 133 LEU A 151 1 19 HELIX 5 5 THR A 166 GLU A 187 1 22 HELIX 6 6 ASN A 199 PHE A 202 5 4 HELIX 7 7 ILE A 229 THR A 237 1 9 HELIX 8 8 VAL A 248 GLY A 254 1 7 HELIX 9 9 ASP A 257 HIS A 265 1 9 HELIX 10 10 ASN A 287 GLY A 299 1 13 HELIX 11 11 THR A 315 ALA A 330 1 16 SHEET 1 A 9 GLY A 47 GLN A 49 0 SHEET 2 A 9 LYS A 76 LEU A 79 1 O LYS A 76 N LEU A 48 SHEET 3 A 9 LYS A 105 HIS A 110 1 O LYS A 105 N LEU A 77 SHEET 4 A 9 TYR A 155 GLN A 158 1 O ILE A 157 N SER A 109 SHEET 5 A 9 PHE A 193 HIS A 196 1 O HIS A 196 N GLN A 158 SHEET 6 A 9 VAL A 242 ASP A 247 1 O GLU A 245 N TYR A 195 SHEET 7 A 9 ILE A 269 ILE A 274 1 O HIS A 273 N MSE A 246 SHEET 8 A 9 TYR A 303 VAL A 305 1 O PHE A 304 N ILE A 274 SHEET 9 A 9 GLY A 47 GLN A 49 1 N GLN A 49 O VAL A 305 SHEET 1 B 3 TYR A 82 GLY A 83 0 SHEET 2 B 3 ALA A 86 ILE A 87 -1 O ALA A 86 N GLY A 83 SHEET 3 B 3 VAL A 90 PRO A 91 -1 O VAL A 90 N ILE A 87 SHEET 1 C 2 ARG A 204 VAL A 205 0 SHEET 2 C 2 ASP A 227 GLN A 228 -1 O ASP A 227 N VAL A 205 LINK C MSE A 72 N GLY A 73 1555 1555 1.33 LINK C MSE A 93 N ASP A 94 1555 1555 1.33 LINK C MSE A 98 N ALA A 99 1555 1555 1.32 LINK C AMSE A 125 N ILE A 126 1555 1555 1.33 LINK C BMSE A 125 N ILE A 126 1555 1555 1.33 LINK C MSE A 138 N AGLU A 139 1555 1555 1.33 LINK C MSE A 138 N BGLU A 139 1555 1555 1.33 LINK C MSE A 161 N PRO A 162 1555 1555 1.37 LINK C MSE A 200 N GLU A 201 1555 1555 1.32 LINK C MSE A 223 N LYS A 224 1555 1555 1.33 LINK C MSE A 233 N LEU A 234 1555 1555 1.32 LINK C MSE A 246 N ASP A 247 1555 1555 1.32 LINK C MSE A 253 N GLY A 254 1555 1555 1.34 LINK C AMSE A 262 N GLN A 263 1555 1555 1.33 LINK C BMSE A 262 N GLN A 263 1555 1555 1.34 LINK C MSE A 286 N ASN A 287 1555 1555 1.31 LINK C MSE A 290 N ILE A 291 1555 1555 1.34 LINK C MSE A 295 N TYR A 296 1555 1555 1.34 LINK C MSE A 310 N PRO A 311 1555 1555 1.34 LINK OD2 ASP A 247 MG MG A 1 1555 1555 1.99 LINK OE1 GLU A 306 MG MG A 1 1555 1555 1.99 LINK MG MG A 1 O HOH A 14 1555 1555 2.13 LINK MG MG A 1 O HOH A 15 1555 1555 2.37 LINK C ASP A 71 N MSE A 72 1555 1555 1.33 LINK C PRO A 91 N MSE A 92 1555 1555 1.33 LINK C MSE A 92 N MSE A 93 1555 1555 1.33 LINK C LYS A 97 N MSE A 98 1555 1555 1.34 LINK C ALA A 124 N AMSE A 125 1555 1555 1.34 LINK C ALA A 124 N BMSE A 125 1555 1555 1.32 LINK C ILE A 137 N MSE A 138 1555 1555 1.33 LINK C PRO A 159 N MSE A 160 1555 1555 1.34 LINK C MSE A 160 N MSE A 161 1555 1555 1.33 LINK C ASN A 199 N MSE A 200 1555 1555 1.33 LINK C PHE A 222 N MSE A 223 1555 1555 1.33 LINK C LEU A 232 N MSE A 233 1555 1555 1.34 LINK C GLU A 245 N MSE A 246 1555 1555 1.34 LINK C VAL A 252 N MSE A 253 1555 1555 1.33 LINK C TYR A 261 N AMSE A 262 1555 1555 1.33 LINK C TYR A 261 N BMSE A 262 1555 1555 1.33 LINK C GLY A 284 N MSE A 285 1555 1555 1.33 LINK C MSE A 285 N MSE A 286 1555 1555 1.30 LINK C GLU A 289 N MSE A 290 1555 1555 1.33 LINK C GLN A 294 N MSE A 295 1555 1555 1.33 LINK C GLN A 309 N MSE A 310 1555 1555 1.32 SITE 1 AC1 6 HOH A 14 HOH A 15 HIS A 196 ASP A 247 SITE 2 AC1 6 HIS A 273 GLU A 306 SITE 1 AC2 2 ASP A 71 MSE A 72 SITE 1 AC3 3 EDO A 6 LYS A 241 LYS A 321 SITE 1 AC4 5 TYR A 82 GLY A 83 LYS A 84 TYR A 140 SITE 2 AC4 5 THR A 144 SITE 1 AC5 5 GLU A 45 GLY A 47 LYS A 76 ASP A 302 SITE 2 AC5 5 TYR A 303 SITE 1 AC6 5 EDO A 3 ASN A 178 ASP A 182 LYS A 241 SITE 2 AC6 5 HOH A 460 CRYST1 77.657 56.634 78.188 90.00 102.98 90.00 C 1 2 1 4 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 0.012877 0.000000 0.002967 0.00000 SCALE2 0.000000 0.017657 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013125 0.00000 MASTER 418 0 25 11 14 0 10 6 0 0 0 24 END