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 5 01-FEB-23 3L23 1 REMARK SEQADV LINK 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 HOH A 14 O REMARK 620 2 HOH A 15 O 78.6 REMARK 620 3 ASP A 247 OD2 87.2 165.8 REMARK 620 4 GLU A 306 OE1 90.1 84.7 95.3 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 EXPRESSION TAG 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 ASP A 71 N MSE A 72 1555 1555 1.33 LINK C MSE A 72 N GLY A 73 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 MSE A 93 N ASP A 94 1555 1555 1.33 LINK C LYS A 97 N MSE A 98 1555 1555 1.34 LINK C MSE A 98 N ALA A 99 1555 1555 1.32 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 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 ILE A 137 N MSE A 138 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 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 MSE A 161 N PRO A 162 1555 1555 1.37 LINK C ASN A 199 N MSE A 200 1555 1555 1.33 LINK C MSE A 200 N GLU A 201 1555 1555 1.32 LINK C PHE A 222 N MSE A 223 1555 1555 1.33 LINK C MSE A 223 N LYS A 224 1555 1555 1.33 LINK C LEU A 232 N MSE A 233 1555 1555 1.34 LINK C MSE A 233 N LEU A 234 1555 1555 1.32 LINK C GLU A 245 N MSE A 246 1555 1555 1.34 LINK C MSE A 246 N ASP A 247 1555 1555 1.32 LINK C VAL A 252 N MSE A 253 1555 1555 1.33 LINK C MSE A 253 N GLY A 254 1555 1555 1.34 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 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 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 MSE A 286 N ASN A 287 1555 1555 1.31 LINK C GLU A 289 N MSE A 290 1555 1555 1.33 LINK C MSE A 290 N ILE A 291 1555 1555 1.34 LINK C GLN A 294 N MSE A 295 1555 1555 1.33 LINK C MSE A 295 N TYR A 296 1555 1555 1.34 LINK C GLN A 309 N MSE A 310 1555 1555 1.32 LINK C MSE A 310 N PRO A 311 1555 1555 1.34 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 MG MG A 1 OD2 ASP A 247 1555 1555 1.99 LINK MG MG A 1 OE1 GLU A 306 1555 1555 1.99 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