HEADER HYDROLASE 22-DEC-09 3L5K TITLE THE CRYSTAL STRUCTURE OF HUMAN HALOACID DEHALOGENASE-LIKE HYDROLASE TITLE 2 DOMAIN CONTAINING 1A (HDHD1A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN-CONTAINING COMPND 3 PROTEIN 1A; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: PROTEIN GS1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: HDHD1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)-R3; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS HDHD1A, HALOACID DEHALOGENASE-LIKE HYDROLASE DOMAIN CONTAINING 1A, KEYWDS 2 HYDROLASE, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, KEYWDS 3 POLYMORPHISM EXPDTA X-RAY DIFFRACTION AUTHOR E.UGOCHUKWU,K.GUO,S.PICAUD,J.MUNIZ,C.ALLERSTON,F.VON DELFT,C.BOUNTRA, AUTHOR 2 C.H.ARROWSMITH,J.WEIGELT,A.EDWARDS,W.W.YUE,K.L.KAVANAGH,U.OPPERMANN, AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 06-SEP-23 3L5K 1 REMARK SEQADV LINK REVDAT 2 01-NOV-17 3L5K 1 REMARK REVDAT 1 09-MAR-10 3L5K 0 JRNL AUTH E.UGOCHUKWU,K.GUO,S.PICAUD,J.MUNIZ,C.ALLERSTON,F.VON DELFT, JRNL AUTH 2 C.BOUNTRA,C.H.ARROWSMITH,J.WEIGELT,A.EDWARDS,W.W.YUE, JRNL AUTH 3 K.L.KAVANAGH,U.OPPERMANN, JRNL AUTH 4 STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL THE CRYSTAL STRUCTURE OF HUMAN HALOACID DEHALOGENASE-LIKE JRNL TITL 2 HYDROLASE DOMAIN CONTAINING 1A (HDHD1A) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0089 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 28009 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1495 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2009 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 121 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1815 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 217 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.81000 REMARK 3 B22 (A**2) : 0.81000 REMARK 3 B33 (A**2) : -1.21000 REMARK 3 B12 (A**2) : 0.40000 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): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.824 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1887 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1296 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2562 ; 1.610 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3195 ; 0.967 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 240 ; 5.267 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;37.768 ;24.872 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 332 ;15.046 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;24.654 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 290 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2068 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 354 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1183 ; 4.763 ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 462 ; 2.013 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1920 ; 6.212 ; 7.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 704 ;10.269 ; 9.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 638 ;12.040 ;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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 20 A 43 REMARK 3 RESIDUE RANGE : A 110 A 250 REMARK 3 ORIGIN FOR THE GROUP (A): -1.6394 37.8950 23.3434 REMARK 3 T TENSOR REMARK 3 T11: 0.0080 T22: 0.0545 REMARK 3 T33: 0.0188 T12: 0.0029 REMARK 3 T13: -0.0019 T23: 0.0203 REMARK 3 L TENSOR REMARK 3 L11: 2.0870 L22: 2.7567 REMARK 3 L33: 3.1085 L12: 0.4907 REMARK 3 L13: 0.2138 L23: 0.3086 REMARK 3 S TENSOR REMARK 3 S11: 0.0464 S12: 0.1048 S13: -0.0043 REMARK 3 S21: -0.0723 S22: -0.0139 S23: -0.1103 REMARK 3 S31: 0.0740 S32: 0.0742 S33: -0.0324 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 44 A 109 REMARK 3 ORIGIN FOR THE GROUP (A): 0.3809 61.9910 14.9082 REMARK 3 T TENSOR REMARK 3 T11: 0.1607 T22: 0.0353 REMARK 3 T33: 0.0916 T12: -0.0273 REMARK 3 T13: -0.0058 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 3.0392 L22: 2.1069 REMARK 3 L33: 7.1363 L12: 0.6354 REMARK 3 L13: 0.5974 L23: -0.7137 REMARK 3 S TENSOR REMARK 3 S11: -0.0986 S12: 0.0303 S13: -0.0563 REMARK 3 S21: 0.0617 S22: 0.0679 S23: -0.1634 REMARK 3 S31: -0.3908 S32: 0.1232 S33: 0.0307 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3L5K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000056860. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29508 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 42.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : 0.10700 REMARK 200 FOR THE DATA SET : 9.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.85500 REMARK 200 R SYM FOR SHELL (I) : 0.85500 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2PIB, 3HLT, 3K1Z, 2W4M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM DIHYDROGEN PHOSPHATE, REMARK 280 1.344 M DI-POTASSIUM HYDROGEN PHOSPHATE, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 34.34333 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 68.68667 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 68.68667 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 34.34333 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 MET A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 GLY A -12 REMARK 465 VAL A -11 REMARK 465 ASP A -10 REMARK 465 LEU A -9 REMARK 465 GLY A -8 REMARK 465 THR A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 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 83 CE NZ REMARK 470 ARG A 201 NE CZ NH1 NH2 REMARK 470 GLU A 228 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 264 O HOH A 267 1.80 REMARK 500 O HOH A 335 O HOH A 395 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 ASP A 141 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES 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 0 164.70 174.77 REMARK 500 ASP A 21 45.58 -82.38 REMARK 500 VAL A 194 79.65 -118.52 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 K A 229 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 14 OD2 REMARK 620 2 ASP A 16 O 83.9 REMARK 620 3 ASP A 176 OD1 133.7 78.5 REMARK 620 4 HOH A 298 O 90.4 164.8 115.1 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 K A 229 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 230 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 231 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 232 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 233 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 234 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PIB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF PUTATIVE BETA-PHOSPHOGLUCOMUTASE FROM REMARK 900 THERMOTOGA MARITIMA REMARK 900 RELATED ID: 3HLT RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF HUMAN HALOACID DEHALOGENASE-LIKE HYDROLASE REMARK 900 DOMAIN CONTAINING 2 (HDHD2) REMARK 900 RELATED ID: 3K1Z RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN HALOACID DEHALOGENASE-LIKE HYDROLASE REMARK 900 DOMAIN CONTAINING 3 (HDHD3) REMARK 900 RELATED ID: 2W4M RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF HUMAN N-ACETYLNEURAMINIC ACID PHOSPHATASE, REMARK 900 NANP DBREF 3L5K A 1 228 UNP Q08623 HDD1A_HUMAN 1 228 SEQADV 3L5K MET A -21 UNP Q08623 EXPRESSION TAG SEQADV 3L5K HIS A -20 UNP Q08623 EXPRESSION TAG SEQADV 3L5K HIS A -19 UNP Q08623 EXPRESSION TAG SEQADV 3L5K HIS A -18 UNP Q08623 EXPRESSION TAG SEQADV 3L5K HIS A -17 UNP Q08623 EXPRESSION TAG SEQADV 3L5K HIS A -16 UNP Q08623 EXPRESSION TAG SEQADV 3L5K HIS A -15 UNP Q08623 EXPRESSION TAG SEQADV 3L5K SER A -14 UNP Q08623 EXPRESSION TAG SEQADV 3L5K SER A -13 UNP Q08623 EXPRESSION TAG SEQADV 3L5K GLY A -12 UNP Q08623 EXPRESSION TAG SEQADV 3L5K VAL A -11 UNP Q08623 EXPRESSION TAG SEQADV 3L5K ASP A -10 UNP Q08623 EXPRESSION TAG SEQADV 3L5K LEU A -9 UNP Q08623 EXPRESSION TAG SEQADV 3L5K GLY A -8 UNP Q08623 EXPRESSION TAG SEQADV 3L5K THR A -7 UNP Q08623 EXPRESSION TAG SEQADV 3L5K GLU A -6 UNP Q08623 EXPRESSION TAG SEQADV 3L5K ASN A -5 UNP Q08623 EXPRESSION TAG SEQADV 3L5K LEU A -4 UNP Q08623 EXPRESSION TAG SEQADV 3L5K TYR A -3 UNP Q08623 EXPRESSION TAG SEQADV 3L5K PHE A -2 UNP Q08623 EXPRESSION TAG SEQADV 3L5K GLN A -1 UNP Q08623 EXPRESSION TAG SEQADV 3L5K SER A 0 UNP Q08623 EXPRESSION TAG SEQADV 3L5K ARG A 116 UNP Q08623 GLY 116 CONFLICT SEQRES 1 A 250 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 250 GLY THR GLU ASN LEU TYR PHE GLN SER MET ALA ALA PRO SEQRES 3 A 250 PRO GLN PRO VAL THR HIS LEU ILE PHE ASP MET ASP GLY SEQRES 4 A 250 LEU LEU LEU ASP THR GLU ARG LEU TYR SER VAL VAL PHE SEQRES 5 A 250 GLN GLU ILE CYS ASN ARG TYR ASP LYS LYS TYR SER TRP SEQRES 6 A 250 ASP VAL LYS SER LEU VAL MET GLY LYS LYS ALA LEU GLU SEQRES 7 A 250 ALA ALA GLN ILE ILE ILE ASP VAL LEU GLN LEU PRO MET SEQRES 8 A 250 SER LYS GLU GLU LEU VAL GLU GLU SER GLN THR LYS LEU SEQRES 9 A 250 LYS GLU VAL PHE PRO THR ALA ALA LEU MET PRO GLY ALA SEQRES 10 A 250 GLU LYS LEU ILE ILE HIS LEU ARG LYS HIS GLY ILE PRO SEQRES 11 A 250 PHE ALA LEU ALA THR SER SER ARG SER ALA SER PHE ASP SEQRES 12 A 250 MET LYS THR SER ARG HIS LYS GLU PHE PHE SER LEU PHE SEQRES 13 A 250 SER HIS ILE VAL LEU GLY ASP ASP PRO GLU VAL GLN HIS SEQRES 14 A 250 GLY LYS PRO ASP PRO ASP ILE PHE LEU ALA CYS ALA LYS SEQRES 15 A 250 ARG PHE SER PRO PRO PRO ALA MET GLU LYS CYS LEU VAL SEQRES 16 A 250 PHE GLU ASP ALA PRO ASN GLY VAL GLU ALA ALA LEU ALA SEQRES 17 A 250 ALA GLY MET GLN VAL VAL MET VAL PRO ASP GLY ASN LEU SEQRES 18 A 250 SER ARG ASP LEU THR THR LYS ALA THR LEU VAL LEU ASN SEQRES 19 A 250 SER LEU GLN ASP PHE GLN PRO GLU LEU PHE GLY LEU PRO SEQRES 20 A 250 SER TYR GLU HET K A 229 1 HET GOL A 230 6 HET CL A 231 1 HET CL A 232 1 HET CL A 233 1 HET CL A 234 1 HETNAM K POTASSIUM ION HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 K K 1+ FORMUL 3 GOL C3 H8 O3 FORMUL 4 CL 4(CL 1-) FORMUL 8 HOH *217(H2 O) HELIX 1 1 ASP A 21 TYR A 37 1 17 HELIX 2 2 SER A 42 MET A 50 1 9 HELIX 3 3 LYS A 53 GLN A 66 1 14 HELIX 4 4 SER A 70 PHE A 86 1 17 HELIX 5 5 PRO A 87 ALA A 89 5 3 HELIX 6 6 GLY A 94 HIS A 105 1 12 HELIX 7 7 ARG A 116 THR A 124 1 9 HELIX 8 8 HIS A 127 SER A 132 1 6 HELIX 9 9 PRO A 152 ARG A 161 1 10 HELIX 10 10 ALA A 167 GLU A 169 5 3 HELIX 11 11 ALA A 177 ALA A 187 1 11 HELIX 12 12 SER A 200 THR A 204 5 5 HELIX 13 13 SER A 213 PHE A 217 5 5 HELIX 14 14 GLN A 218 GLY A 223 5 6 SHEET 1 A 7 SER A 0 MET A 1 0 SHEET 2 A 7 LEU A 209 VAL A 210 -1 O VAL A 210 N SER A 0 SHEET 3 A 7 GLN A 190 MET A 193 1 N MET A 193 O LEU A 209 SHEET 4 A 7 CYS A 171 GLU A 175 1 N VAL A 173 O VAL A 192 SHEET 5 A 7 HIS A 10 ASP A 14 1 N ILE A 12 O LEU A 172 SHEET 6 A 7 PHE A 109 ALA A 112 1 O ALA A 112 N PHE A 13 SHEET 7 A 7 ILE A 137 VAL A 138 1 O VAL A 138 N LEU A 111 LINK OD2 ASP A 14 K K A 229 1555 1555 2.90 LINK O ASP A 16 K K A 229 1555 1555 2.69 LINK OD1 ASP A 176 K K A 229 1555 1555 2.58 LINK K K A 229 O HOH A 298 1555 1555 2.88 CISPEP 1 LYS A 149 PRO A 150 0 9.99 CISPEP 2 SER A 163 PRO A 164 0 -2.27 SITE 1 AC1 5 ASP A 14 ASP A 16 GLU A 175 ASP A 176 SITE 2 AC1 5 HOH A 298 SITE 1 AC2 5 SER A 132 PHE A 134 SER A 135 ASP A 202 SITE 2 AC2 5 HOH A 307 SITE 1 AC3 3 TYR A 41 TRP A 43 LYS A 46 SITE 1 AC4 3 ARG A 116 SER A 119 HOH A 250 SITE 1 AC5 1 GLY A 148 SITE 1 AC6 1 ALA A 54 CRYST1 85.190 85.190 103.030 90.00 90.00 120.00 P 31 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 0.011739 0.006777 0.000000 0.00000 SCALE2 0.000000 0.013554 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009706 0.00000