HEADER HYDROLASE 21-JUN-17 5XTU TITLE CRYSTAL STRUCTURE OF GDSL ESTERASE OF PHOTOBACTERIUM SP. J15 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GDSL-FAMILY ESTERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHOTOBACTERIUM SP. J15(2011); SOURCE 3 ORGANISM_TAXID: 1109422; SOURCE 4 STRAIN: 2011; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTAGAMI(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32B KEYWDS GDSL, SGNH, ESTERASE, HYDROLASE, PHOTOBACTERIUM EXPDTA X-RAY DIFFRACTION AUTHOR S.N.H.S.MAZLAN,M.A.JONET,T.C.LEOW,M.S.M.ALI,R.N.Z.R.A.RAHMAN REVDAT 2 17-OCT-18 5XTU 1 COMPND AUTHOR REVDAT 1 10-OCT-18 5XTU 0 JRNL AUTH S.N.H.S.MAZLAN,M.S.M.ALI,R.N.Z.R.A.RAHMAN,S.SABRI,M.A.JONET, JRNL AUTH 2 T.C.LEOW JRNL TITL CRYSTALLIZATION AND STRUCTURE ELUCIDATION OF GDSL ESTERASE JRNL TITL 2 OF PHOTOBACTERIUM SP. J15. JRNL REF INT. J. BIOL. MACROMOL. V. 119 1188 2018 JRNL REFN ISSN 1879-0003 JRNL PMID 30102982 JRNL DOI 10.1016/J.IJBIOMAC.2018.08.022 REMARK 2 REMARK 2 RESOLUTION. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 67010 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3478 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) : 1.38 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.42 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4713 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 257 REMARK 3 BIN FREE R VALUE : 0.2180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2516 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 436 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.36000 REMARK 3 B33 (A**2) : 0.37000 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): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.054 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.032 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.773 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2661 ; 0.029 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2502 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3612 ; 2.524 ; 1.939 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5747 ; 1.183 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 341 ; 6.205 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;38.138 ;25.203 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 430 ;13.269 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;13.929 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 391 ; 0.154 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3108 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 635 ; 0.003 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5XTU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1300004171. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70491 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 56.230 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.98 REMARK 200 R MERGE FOR SHELL (I) : 0.19300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.10 M AMMONIUM SULPHATE, 0.15 M REMARK 280 SODIUM CACODYLATE TRIHYDRATE PH 6.5, AND 20% PEG 8000, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 24.59100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.73400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.23050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.73400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.59100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.23050 REMARK 290 SMTRY3 4 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 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 TOTAL BURIED SURFACE AREA: 300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 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 -31 REMARK 465 SER A -30 REMARK 465 GLY A -29 REMARK 465 MET A -28 REMARK 465 LYS A -27 REMARK 465 GLU A -26 REMARK 465 THR A -25 REMARK 465 ALA A -24 REMARK 465 ALA A -23 REMARK 465 ALA A -22 REMARK 465 LYS A -21 REMARK 465 PHE A -20 REMARK 465 GLU A -19 REMARK 465 ARG A -18 REMARK 465 GLN A -17 REMARK 465 HIS A -16 REMARK 465 MET A -15 REMARK 465 ASP A -14 REMARK 465 SER A -13 REMARK 465 PRO A -12 REMARK 465 ASP A -11 REMARK 465 LEU A -10 REMARK 465 GLY A -9 REMARK 465 THR A -8 REMARK 465 ASP A -7 REMARK 465 ASP A -6 REMARK 465 ASP A -5 REMARK 465 ASP A -4 REMARK 465 LYS A -3 REMARK 465 ALA A -2 REMARK 465 MET A -1 REMARK 465 VAL A 0 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 AS CAC A 404 O HOH A 504 1.08 REMARK 500 C1 CAC A 404 O HOH A 504 1.47 REMARK 500 NZ LYS A 312 O HOH A 501 1.75 REMARK 500 NH1 ARG A 297 O HOH A 502 1.82 REMARK 500 C2 CAC A 404 O HOH A 504 1.95 REMARK 500 O HOH A 829 O HOH A 923 2.02 REMARK 500 OG SER A 320 O HOH A 503 2.13 REMARK 500 O HOH A 700 O HOH A 833 2.14 REMARK 500 O HOH A 860 O HOH A 924 2.16 REMARK 500 C TYR A 286 O HOH A 508 2.16 REMARK 500 O2 CAC A 404 O HOH A 504 2.18 REMARK 500 OE1 GLN A 28 O HOH A 505 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 841 O HOH A 860 4555 2.06 REMARK 500 REMARK 500 REMARK: NULL 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 SER A 75 CB SER A 75 OG -0.086 REMARK 500 TRP A 101 CE2 TRP A 101 CD2 -0.072 REMARK 500 TYR A 286 CG TYR A 286 CD2 0.087 REMARK 500 TYR A 286 CZ TYR A 286 CE2 0.080 REMARK 500 SER A 324 CA SER A 324 CB -0.111 REMARK 500 ARG A 326 CG ARG A 326 CD 0.173 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 39 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 68 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 81 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 PHE A 211 CB - CG - CD1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 220 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 326 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 LEU A 328 CA - C - O ANGL. DEV. = -12.7 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 ASP A 11 -160.30 -125.49 REMARK 500 SER A 48 -179.52 -171.42 REMARK 500 ASP A 115 47.07 -160.47 REMARK 500 TYR A 286 13.49 -67.19 REMARK 500 ASP A 302 -144.38 -113.30 REMARK 500 LEU A 304 -49.23 -151.56 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 PEG A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CAC A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CAC A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 408 DBREF1 5XTU A 1 328 UNP A0A0K0PV22_9GAMM DBREF2 5XTU A A0A0K0PV22 20 347 SEQADV 5XTU GLY A -31 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU SER A -30 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU GLY A -29 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU MET A -28 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU LYS A -27 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU GLU A -26 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU THR A -25 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU ALA A -24 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU ALA A -23 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU ALA A -22 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU LYS A -21 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU PHE A -20 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU GLU A -19 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU ARG A -18 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU GLN A -17 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU HIS A -16 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU MET A -15 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU ASP A -14 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU SER A -13 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU PRO A -12 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU ASP A -11 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU LEU A -10 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU GLY A -9 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU THR A -8 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU ASP A -7 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU ASP A -6 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU ASP A -5 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU ASP A -4 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU LYS A -3 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU ALA A -2 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU MET A -1 UNP A0A0K0PV2 EXPRESSION TAG SEQADV 5XTU VAL A 0 UNP A0A0K0PV2 EXPRESSION TAG SEQRES 1 A 360 GLY SER GLY MET LYS GLU THR ALA ALA ALA LYS PHE GLU SEQRES 2 A 360 ARG GLN HIS MET ASP SER PRO ASP LEU GLY THR ASP ASP SEQRES 3 A 360 ASP ASP LYS ALA MET VAL ALA GLU PHE ASP ARG ILE THR SEQRES 4 A 360 ASN PHE GLY ASP SER LEU SER ASP ILE GLY ASN LYS HIS SEQRES 5 A 360 MET ILE THR VAL ASP MET ASN GLN ALA THR SER GLY LYS SEQRES 6 A 360 ILE GLY ILE ARG ALA ASP LYS PRO ASN PHE ASP GLY ARG SEQRES 7 A 360 PHE SER ASN GLY PRO VAL TRP THR GLU TYR LEU ALA GLY SEQRES 8 A 360 PHE LEU ALA LYS PRO ALA PRO VAL ARG GLY HIS GLY GLU SEQRES 9 A 360 ILE ASP SER GLN VAL VAL LEU LYS ASP GLN ALA GLY LYS SEQRES 10 A 360 GLN ILE THR TYR HIS TYR HIS HIS ASN ALA LEU PRO GLY SEQRES 11 A 360 THR ASN TRP ALA VAL GLY GLY ALA MET SER GLY LEU GLY SEQRES 12 A 360 ASN PHE LEU ASP ILE ASP ALA ALA ASN GLY PHE THR ALA SEQRES 13 A 360 LYS SER GLY LEU ASP VAL LEU THR ASN THR GLY GLN GLN SEQRES 14 A 360 ILE LYS LEU ARG ILE ALA ASN LYS GLY GLN PHE THR GLY SEQRES 15 A 360 ASN GLU LEU VAL SER TYR MET SER GLY THR ASN ASN LEU SEQRES 16 A 360 TRP PHE THR LEU PHE GLY ASP LEU ASP GLN THR GLY ASN SEQRES 17 A 360 LYS ALA ALA GLY PHE ALA LEU THR ASP ILE GLU THR LEU SEQRES 18 A 360 ILE ASP ALA GLY ALA LYS GLN VAL LEU ALA ALA ASN ILE SEQRES 19 A 360 PRO ASP PHE VAL ASP ALA PRO TRP PHE ALA GLY GLN GLN SEQRES 20 A 360 LYS LYS THR THR ARG PHE ILE GLN SER HIS ASN GLN ALA SEQRES 21 A 360 LEU LYS ALA GLY LEU ASP GLN LEU ALA ALA ALA HIS PRO SEQRES 22 A 360 ASP VAL GLU ILE TYR TYR PHE ASP ALA PHE ASP LEU PHE SEQRES 23 A 360 ASN LYS VAL SER ASN GLU VAL LYS THR LYS GLY LYS TYR SEQRES 24 A 360 GLN ASP LYS GLU LEU ALA ILE THR LEU THR ASN VAL THR SEQRES 25 A 360 GLY GLU ALA TYR SER TYR ALA THR GLY LYS VAL ILE ALA SEQRES 26 A 360 GLN PRO ASN ARG ASN LEU PHE TRP ASP GLY LEU HIS PRO SEQRES 27 A 360 THR THR ALA MET HIS LYS ILE MET ALA LYS GLU ALA ALA SEQRES 28 A 360 SER LEU VAL ILE SER GLY ARG THR LEU HET PEG A 401 7 HET CL A 402 1 HET CAC A 403 5 HET CAC A 404 5 HET CA A 405 1 HET EDO A 406 4 HET PO4 A 407 4 HET PO4 A 408 5 HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM CL CHLORIDE ION HETNAM CAC CACODYLATE ION HETNAM CA CALCIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM PO4 PHOSPHATE ION HETSYN CAC DIMETHYLARSINATE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 PEG C4 H10 O3 FORMUL 3 CL CL 1- FORMUL 4 CAC 2(C2 H6 AS O2 1-) FORMUL 6 CA CA 2+ FORMUL 7 EDO C2 H6 O2 FORMUL 8 PO4 2(O4 P 3-) FORMUL 10 HOH *436(H2 O) HELIX 1 AA1 GLY A 17 THR A 30 1 14 HELIX 2 AA2 VAL A 52 ALA A 62 1 11 HELIX 3 AA3 ASN A 133 GLY A 146 1 14 HELIX 4 AA4 GLY A 159 GLY A 169 1 11 HELIX 5 AA5 THR A 174 ALA A 192 1 19 HELIX 6 AA6 ALA A 208 ALA A 212 5 5 HELIX 7 AA7 GLN A 214 HIS A 240 1 27 HELIX 8 AA8 ASP A 249 GLY A 265 1 17 HELIX 9 AA9 GLN A 294 ASN A 298 5 5 HELIX 10 AB1 THR A 307 SER A 324 1 18 SHEET 1 AA1 4 ARG A 5 GLY A 10 0 SHEET 2 AA1 4 GLU A 152 MET A 157 1 O SER A 155 N THR A 7 SHEET 3 AA1 4 GLN A 196 ALA A 200 1 O LEU A 198 N VAL A 154 SHEET 4 AA1 4 GLU A 244 PHE A 248 1 O TYR A 246 N VAL A 197 SHEET 1 AA2 3 GLN A 86 HIS A 93 0 SHEET 2 AA2 3 ILE A 73 LYS A 80 -1 N LEU A 79 O ILE A 87 SHEET 3 AA2 3 THR A 123 SER A 126 -1 O LYS A 125 N VAL A 78 SHEET 1 AA3 2 ASN A 112 PHE A 113 0 SHEET 2 AA3 2 LEU A 131 THR A 132 -1 O LEU A 131 N PHE A 113 SHEET 1 AA4 2 TYR A 267 ASP A 269 0 SHEET 2 AA4 2 ILE A 274 LEU A 276 -1 O LEU A 276 N TYR A 267 LINK O1 CAC A 403 CA CA A 405 1555 1555 2.12 LINK OG SER A 12 P PO4 A 407 1555 1555 1.90 CISPEP 1 LYS A 40 PRO A 41 0 14.43 SITE 1 AC1 8 ALA A 58 GLY A 59 ALA A 62 LYS A 63 SITE 2 AC1 8 ALA A 65 HOH A 599 HOH A 635 HOH A 695 SITE 1 AC2 5 THR A 7 GLY A 98 THR A 99 ARG A 141 SITE 2 AC2 5 LYS A 145 SITE 1 AC3 10 LYS A 19 GLY A 105 ASP A 115 TRP A 164 SITE 2 AC3 10 PHE A 165 CA A 405 PO4 A 407 HOH A 514 SITE 3 AC3 10 HOH A 515 HOH A 536 SITE 1 AC4 7 HIS A 90 GLN A 147 ASP A 191 ALA A 192 SITE 2 AC4 7 GLY A 193 HOH A 504 HOH A 696 SITE 1 AC5 3 ASN A 161 CAC A 403 PO4 A 407 SITE 1 AC6 6 GLY A 213 GLN A 214 GLN A 215 LYS A 216 SITE 2 AC6 6 LYS A 217 HOH A 511 SITE 1 AC7 7 ASP A 11 SER A 12 GLY A 105 ASN A 161 SITE 2 AC7 7 HIS A 305 CAC A 403 CA A 405 SITE 1 AC8 9 GLN A 294 ASN A 296 ARG A 297 HOH A 507 SITE 2 AC8 9 HOH A 533 HOH A 580 HOH A 608 HOH A 713 SITE 3 AC8 9 HOH A 752 CRYST1 49.182 66.461 105.468 90.00 90.00 90.00 P 21 21 21 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 0.020333 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015046 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009482 0.00000