HEADER HYDROLASE 13-JAN-14 4OEC TITLE CRYSTAL STRUCTURE OF GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE FROM TITLE 2 THERMOCOCCUS KODAKARENSIS KOD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCEROPHOSPHORYL DIESTER PHOSPHODIESTERASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: 3.1.4.46; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS KODAKARENSIS; SOURCE 3 ORGANISM_TAXID: 69014; SOURCE 4 STRAIN: KOD1; SOURCE 5 GENE: TK1397; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET25B KEYWDS TIM BARREL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.ATSUTA,D.J.YOU,K.TAKANO,Y.KOGA,S.KANAYA REVDAT 3 08-NOV-23 4OEC 1 REMARK LINK REVDAT 2 22-NOV-17 4OEC 1 REMARK REVDAT 1 14-JAN-15 4OEC 0 JRNL AUTH Y.ATSUTA,D.J.YOU,K.TAKANO,Y.KOGA,S.KANAYA JRNL TITL CRYSTAL STRUCTURE OF GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE JRNL TITL 2 FROM THERMOCOCCUS KODAKARENSIS KOD1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 79606 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3998 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5316 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.70 REMARK 3 BIN R VALUE (WORKING SET) : 0.2130 REMARK 3 BIN FREE R VALUE SET COUNT : 277 REMARK 3 BIN FREE R VALUE : 0.2410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8016 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 693 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.06 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.08000 REMARK 3 B22 (A**2) : 1.91000 REMARK 3 B33 (A**2) : -2.99000 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): 0.173 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.673 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8140 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11008 ; 0.978 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 988 ; 7.232 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 392 ;32.312 ;24.388 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1560 ;14.998 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 72 ;18.111 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1264 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6036 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 4940 ; 1.507 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 8008 ; 2.335 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3200 ; 3.906 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3000 ; 5.973 ; 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 : NULL 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 U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 4OEC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084385. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : HORIZONTAL FOCUSING MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER SMART 6500 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79998 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 13.60 REMARK 200 R MERGE (I) : 0.14200 REMARK 200 R SYM (I) : 0.14200 REMARK 200 FOR THE DATA SET : 23.4930 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.40 REMARK 200 R MERGE FOR SHELL (I) : 0.55800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP, BALBES REMARK 200 STARTING MODEL: 2OTD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30%(W/V) PEG4000, 0.2M MAGNESIUM REMARK 280 CHLORIDE HEXAHYDRATE, 0.1M TRIS-HCL, PH 8.5, VAPOR DIFFUSION, REMARK 280 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 21.86200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.81950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 66.01700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.81950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.86200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 66.01700 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, 3, 4 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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: 3 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: C 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: 4 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: D 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 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 TYR A 215 CD1 TYR A 215 CE1 -0.091 REMARK 500 GLU D 21 CB GLU D 21 CG -0.194 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 47 O - C - N ANGL. DEV. = -11.9 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 ASP A 47 42.85 -100.04 REMARK 500 PRO B 125 -19.65 -46.02 REMARK 500 GLU D 21 123.31 -31.75 REMARK 500 ASP D 47 46.66 -101.59 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 47 -23.58 REMARK 500 ASP D 47 -13.55 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 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 39 OE2 REMARK 620 2 ASP A 41 OD1 110.1 REMARK 620 3 GLU A 106 OE1 98.7 90.7 REMARK 620 4 HOH A 713 O 86.2 83.6 173.5 REMARK 620 5 HOH A 718 O 92.3 153.4 100.3 83.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 39 OE2 REMARK 620 2 ASP B 41 OD1 110.3 REMARK 620 3 GLU B 106 OE1 100.0 93.9 REMARK 620 4 HOH B 530 O 93.1 151.2 98.5 REMARK 620 5 HOH B 570 O 162.0 81.5 92.4 72.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 39 OE2 REMARK 620 2 ASP C 41 OD1 102.0 REMARK 620 3 GLU C 106 OE2 95.2 94.3 REMARK 620 4 HOH C 592 O 86.9 91.5 173.3 REMARK 620 5 HOH C 606 O 162.2 94.9 88.8 87.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU D 39 OE2 REMARK 620 2 ASP D 41 OD1 110.8 REMARK 620 3 GLU D 106 OE1 98.2 93.5 REMARK 620 4 HOH D 666 O 86.4 84.9 175.4 REMARK 620 5 HOH D 672 O 97.7 147.6 97.7 81.5 REMARK 620 N 1 2 3 4 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG C 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG D 401 DBREF 4OEC A 1 248 UNP Q5JGZ3 Q5JGZ3_THEKO 1 248 DBREF 4OEC B 1 248 UNP Q5JGZ3 Q5JGZ3_THEKO 1 248 DBREF 4OEC C 1 248 UNP Q5JGZ3 Q5JGZ3_THEKO 1 248 DBREF 4OEC D 1 248 UNP Q5JGZ3 Q5JGZ3_THEKO 1 248 SEQRES 1 A 248 MET TRP GLU ARG ASP ARG VAL ILE VAL LEU GLY HIS ARG SEQRES 2 A 248 GLY TYR MET SER ASN TYR PRO GLU ASN THR LEU LEU ALA SEQRES 3 A 248 PHE ARG LYS ALA VAL GLU ALA GLY ALA ASP GLY ILE GLU SEQRES 4 A 248 LEU ASP VAL TRP LEU THR LYS ASP GLY ARG VAL VAL VAL SEQRES 5 A 248 MET HIS ASP GLU THR ILE ASP ARG THR SER ASN MET LYS SEQRES 6 A 248 GLY ARG GLN LYS ASP MET THR LEU GLU GLU LEU LYS LYS SEQRES 7 A 248 ALA ASP VAL GLY GLN GLY GLU ARG ILE PRO THR LEU GLU SEQRES 8 A 248 GLU VAL PHE GLU ALA ILE PRO ARG ASN ALA LEU VAL ASN SEQRES 9 A 248 VAL GLU LEU LYS ASP ARG ASP ALA ALA ARG GLU VAL ALA SEQRES 10 A 248 GLU ILE VAL ALA GLU ASN ASN PRO GLU ARG VAL MET ILE SEQRES 11 A 248 SER SER PHE ASP ILE ASP ALA LEU ARG GLU TYR ARG LYS SEQRES 12 A 248 TYR ASP ASP GLU THR THR MET GLY LEU LEU ILE ASP ARG SEQRES 13 A 248 GLU GLU VAL VAL PRO LEU ILE PRO LYS LEU LYS ASP GLU SEQRES 14 A 248 LEU ASN LEU TRP SER VAL ASN VAL PRO MET GLU ALA ILE SEQRES 15 A 248 PRO LEU ILE GLY LEU GLU LYS THR LEU GLN ALA LEU HIS SEQRES 16 A 248 TRP VAL ARG SER LEU GLY LEU LYS VAL VAL LEU TRP THR SEQRES 17 A 248 GLU ASN ASP VAL LEU PHE TYR LYS ASP ASP ASN LEU ALA SEQRES 18 A 248 LYS LEU LYS GLY LEU PHE GLU VAL VAL ILE ALA ASN ASP SEQRES 19 A 248 VAL VAL ARG MET ILE GLU TYR LEU LYS LYS LEU GLY LEU SEQRES 20 A 248 ARG SEQRES 1 B 248 MET TRP GLU ARG ASP ARG VAL ILE VAL LEU GLY HIS ARG SEQRES 2 B 248 GLY TYR MET SER ASN TYR PRO GLU ASN THR LEU LEU ALA SEQRES 3 B 248 PHE ARG LYS ALA VAL GLU ALA GLY ALA ASP GLY ILE GLU SEQRES 4 B 248 LEU ASP VAL TRP LEU THR LYS ASP GLY ARG VAL VAL VAL SEQRES 5 B 248 MET HIS ASP GLU THR ILE ASP ARG THR SER ASN MET LYS SEQRES 6 B 248 GLY ARG GLN LYS ASP MET THR LEU GLU GLU LEU LYS LYS SEQRES 7 B 248 ALA ASP VAL GLY GLN GLY GLU ARG ILE PRO THR LEU GLU SEQRES 8 B 248 GLU VAL PHE GLU ALA ILE PRO ARG ASN ALA LEU VAL ASN SEQRES 9 B 248 VAL GLU LEU LYS ASP ARG ASP ALA ALA ARG GLU VAL ALA SEQRES 10 B 248 GLU ILE VAL ALA GLU ASN ASN PRO GLU ARG VAL MET ILE SEQRES 11 B 248 SER SER PHE ASP ILE ASP ALA LEU ARG GLU TYR ARG LYS SEQRES 12 B 248 TYR ASP ASP GLU THR THR MET GLY LEU LEU ILE ASP ARG SEQRES 13 B 248 GLU GLU VAL VAL PRO LEU ILE PRO LYS LEU LYS ASP GLU SEQRES 14 B 248 LEU ASN LEU TRP SER VAL ASN VAL PRO MET GLU ALA ILE SEQRES 15 B 248 PRO LEU ILE GLY LEU GLU LYS THR LEU GLN ALA LEU HIS SEQRES 16 B 248 TRP VAL ARG SER LEU GLY LEU LYS VAL VAL LEU TRP THR SEQRES 17 B 248 GLU ASN ASP VAL LEU PHE TYR LYS ASP ASP ASN LEU ALA SEQRES 18 B 248 LYS LEU LYS GLY LEU PHE GLU VAL VAL ILE ALA ASN ASP SEQRES 19 B 248 VAL VAL ARG MET ILE GLU TYR LEU LYS LYS LEU GLY LEU SEQRES 20 B 248 ARG SEQRES 1 C 248 MET TRP GLU ARG ASP ARG VAL ILE VAL LEU GLY HIS ARG SEQRES 2 C 248 GLY TYR MET SER ASN TYR PRO GLU ASN THR LEU LEU ALA SEQRES 3 C 248 PHE ARG LYS ALA VAL GLU ALA GLY ALA ASP GLY ILE GLU SEQRES 4 C 248 LEU ASP VAL TRP LEU THR LYS ASP GLY ARG VAL VAL VAL SEQRES 5 C 248 MET HIS ASP GLU THR ILE ASP ARG THR SER ASN MET LYS SEQRES 6 C 248 GLY ARG GLN LYS ASP MET THR LEU GLU GLU LEU LYS LYS SEQRES 7 C 248 ALA ASP VAL GLY GLN GLY GLU ARG ILE PRO THR LEU GLU SEQRES 8 C 248 GLU VAL PHE GLU ALA ILE PRO ARG ASN ALA LEU VAL ASN SEQRES 9 C 248 VAL GLU LEU LYS ASP ARG ASP ALA ALA ARG GLU VAL ALA SEQRES 10 C 248 GLU ILE VAL ALA GLU ASN ASN PRO GLU ARG VAL MET ILE SEQRES 11 C 248 SER SER PHE ASP ILE ASP ALA LEU ARG GLU TYR ARG LYS SEQRES 12 C 248 TYR ASP ASP GLU THR THR MET GLY LEU LEU ILE ASP ARG SEQRES 13 C 248 GLU GLU VAL VAL PRO LEU ILE PRO LYS LEU LYS ASP GLU SEQRES 14 C 248 LEU ASN LEU TRP SER VAL ASN VAL PRO MET GLU ALA ILE SEQRES 15 C 248 PRO LEU ILE GLY LEU GLU LYS THR LEU GLN ALA LEU HIS SEQRES 16 C 248 TRP VAL ARG SER LEU GLY LEU LYS VAL VAL LEU TRP THR SEQRES 17 C 248 GLU ASN ASP VAL LEU PHE TYR LYS ASP ASP ASN LEU ALA SEQRES 18 C 248 LYS LEU LYS GLY LEU PHE GLU VAL VAL ILE ALA ASN ASP SEQRES 19 C 248 VAL VAL ARG MET ILE GLU TYR LEU LYS LYS LEU GLY LEU SEQRES 20 C 248 ARG SEQRES 1 D 248 MET TRP GLU ARG ASP ARG VAL ILE VAL LEU GLY HIS ARG SEQRES 2 D 248 GLY TYR MET SER ASN TYR PRO GLU ASN THR LEU LEU ALA SEQRES 3 D 248 PHE ARG LYS ALA VAL GLU ALA GLY ALA ASP GLY ILE GLU SEQRES 4 D 248 LEU ASP VAL TRP LEU THR LYS ASP GLY ARG VAL VAL VAL SEQRES 5 D 248 MET HIS ASP GLU THR ILE ASP ARG THR SER ASN MET LYS SEQRES 6 D 248 GLY ARG GLN LYS ASP MET THR LEU GLU GLU LEU LYS LYS SEQRES 7 D 248 ALA ASP VAL GLY GLN GLY GLU ARG ILE PRO THR LEU GLU SEQRES 8 D 248 GLU VAL PHE GLU ALA ILE PRO ARG ASN ALA LEU VAL ASN SEQRES 9 D 248 VAL GLU LEU LYS ASP ARG ASP ALA ALA ARG GLU VAL ALA SEQRES 10 D 248 GLU ILE VAL ALA GLU ASN ASN PRO GLU ARG VAL MET ILE SEQRES 11 D 248 SER SER PHE ASP ILE ASP ALA LEU ARG GLU TYR ARG LYS SEQRES 12 D 248 TYR ASP ASP GLU THR THR MET GLY LEU LEU ILE ASP ARG SEQRES 13 D 248 GLU GLU VAL VAL PRO LEU ILE PRO LYS LEU LYS ASP GLU SEQRES 14 D 248 LEU ASN LEU TRP SER VAL ASN VAL PRO MET GLU ALA ILE SEQRES 15 D 248 PRO LEU ILE GLY LEU GLU LYS THR LEU GLN ALA LEU HIS SEQRES 16 D 248 TRP VAL ARG SER LEU GLY LEU LYS VAL VAL LEU TRP THR SEQRES 17 D 248 GLU ASN ASP VAL LEU PHE TYR LYS ASP ASP ASN LEU ALA SEQRES 18 D 248 LYS LEU LYS GLY LEU PHE GLU VAL VAL ILE ALA ASN ASP SEQRES 19 D 248 VAL VAL ARG MET ILE GLU TYR LEU LYS LYS LEU GLY LEU SEQRES 20 D 248 ARG HET MG A 401 1 HET MG B 401 1 HET MG C 401 1 HET MG D 401 1 HETNAM MG MAGNESIUM ION FORMUL 5 MG 4(MG 2+) FORMUL 9 HOH *693(H2 O) HELIX 1 1 THR A 23 ALA A 33 1 11 HELIX 2 2 ARG A 67 MET A 71 5 5 HELIX 3 3 THR A 72 LYS A 77 1 6 HELIX 4 4 THR A 89 ILE A 97 1 9 HELIX 5 5 ASP A 109 ASP A 111 5 3 HELIX 6 6 ALA A 112 GLU A 122 1 11 HELIX 7 7 ASN A 124 GLU A 126 5 3 HELIX 8 8 ASP A 134 ASP A 145 1 12 HELIX 9 9 ARG A 156 PRO A 161 5 6 HELIX 10 10 LEU A 162 ASN A 171 1 10 HELIX 11 11 GLU A 180 GLY A 186 1 7 HELIX 12 12 GLY A 186 LEU A 200 1 15 HELIX 13 13 THR A 208 ASN A 210 5 3 HELIX 14 14 ASP A 211 LYS A 216 1 6 HELIX 15 15 ASP A 218 LEU A 223 1 6 HELIX 16 16 ASP A 234 LEU A 245 1 12 HELIX 17 17 THR B 23 ALA B 33 1 11 HELIX 18 18 ARG B 67 MET B 71 5 5 HELIX 19 19 THR B 72 LYS B 77 1 6 HELIX 20 20 THR B 89 ILE B 97 1 9 HELIX 21 21 ASP B 109 ASP B 111 5 3 HELIX 22 22 ALA B 112 GLU B 122 1 11 HELIX 23 23 ASN B 123 GLU B 126 5 4 HELIX 24 24 ASP B 134 ASP B 145 1 12 HELIX 25 25 ARG B 156 PRO B 161 5 6 HELIX 26 26 LEU B 162 ASN B 171 1 10 HELIX 27 27 GLU B 180 GLY B 186 1 7 HELIX 28 28 GLY B 186 LEU B 200 1 15 HELIX 29 29 ASP B 211 LYS B 216 1 6 HELIX 30 30 ASP B 218 LEU B 223 1 6 HELIX 31 31 ASP B 234 LEU B 245 1 12 HELIX 32 32 THR C 23 ALA C 33 1 11 HELIX 33 33 ARG C 67 MET C 71 5 5 HELIX 34 34 THR C 72 LYS C 77 1 6 HELIX 35 35 THR C 89 ILE C 97 1 9 HELIX 36 36 ASP C 109 ASP C 111 5 3 HELIX 37 37 ALA C 112 GLU C 122 1 11 HELIX 38 38 ASN C 123 GLU C 126 5 4 HELIX 39 39 ASP C 134 LYS C 143 1 10 HELIX 40 40 ARG C 156 PRO C 161 5 6 HELIX 41 41 LEU C 162 ASN C 171 1 10 HELIX 42 42 GLU C 180 ILE C 185 1 6 HELIX 43 43 GLY C 186 LEU C 200 1 15 HELIX 44 44 ASP C 211 LYS C 216 1 6 HELIX 45 45 ASP C 218 LEU C 223 1 6 HELIX 46 46 ASP C 234 GLY C 246 1 13 HELIX 47 47 THR D 23 ALA D 33 1 11 HELIX 48 48 ARG D 67 MET D 71 5 5 HELIX 49 49 THR D 72 LYS D 77 1 6 HELIX 50 50 THR D 89 ILE D 97 1 9 HELIX 51 51 ASP D 109 ASP D 111 5 3 HELIX 52 52 ALA D 112 GLU D 122 1 11 HELIX 53 53 ASN D 124 GLU D 126 5 3 HELIX 54 54 ASP D 134 ASP D 145 1 12 HELIX 55 55 ARG D 156 PRO D 161 5 6 HELIX 56 56 LEU D 162 ASN D 171 1 10 HELIX 57 57 GLU D 180 GLY D 186 1 7 HELIX 58 58 GLY D 186 LEU D 200 1 15 HELIX 59 59 ASP D 211 LYS D 216 1 6 HELIX 60 60 ASP D 218 LEU D 223 1 6 HELIX 61 61 ASP D 234 LEU D 245 1 12 SHEET 1 A10 VAL A 50 VAL A 52 0 SHEET 2 A10 GLY A 37 LEU A 44 -1 N TRP A 43 O VAL A 51 SHEET 3 A10 LEU A 102 LEU A 107 1 O GLU A 106 N LEU A 40 SHEET 4 A10 VAL A 128 SER A 132 1 O MET A 129 N VAL A 103 SHEET 5 A10 THR A 149 LEU A 153 1 O THR A 149 N ILE A 130 SHEET 6 A10 SER A 174 PRO A 178 1 O ASN A 176 N LEU A 152 SHEET 7 A10 LYS A 203 TRP A 207 1 O VAL A 205 N VAL A 175 SHEET 8 A10 VAL A 229 ALA A 232 1 O VAL A 229 N LEU A 206 SHEET 9 A10 ILE A 8 HIS A 12 1 N ILE A 8 O VAL A 230 SHEET 10 A10 GLY A 37 LEU A 44 1 O GLY A 37 N GLY A 11 SHEET 1 B10 VAL B 50 VAL B 52 0 SHEET 2 B10 GLY B 37 LEU B 44 -1 N TRP B 43 O VAL B 51 SHEET 3 B10 LEU B 102 LEU B 107 1 O GLU B 106 N LEU B 40 SHEET 4 B10 VAL B 128 SER B 132 1 O MET B 129 N VAL B 103 SHEET 5 B10 THR B 149 LEU B 153 1 O THR B 149 N ILE B 130 SHEET 6 B10 SER B 174 PRO B 178 1 O ASN B 176 N LEU B 152 SHEET 7 B10 LYS B 203 TRP B 207 1 O VAL B 205 N VAL B 177 SHEET 8 B10 VAL B 229 ALA B 232 1 O VAL B 229 N LEU B 206 SHEET 9 B10 ILE B 8 HIS B 12 1 N LEU B 10 O VAL B 230 SHEET 10 B10 GLY B 37 LEU B 44 1 O GLU B 39 N GLY B 11 SHEET 1 C10 VAL C 50 VAL C 52 0 SHEET 2 C10 GLY C 37 LEU C 44 -1 N TRP C 43 O VAL C 51 SHEET 3 C10 LEU C 102 LEU C 107 1 O GLU C 106 N LEU C 40 SHEET 4 C10 VAL C 128 SER C 132 1 O SER C 131 N VAL C 105 SHEET 5 C10 THR C 149 LEU C 153 1 O GLY C 151 N ILE C 130 SHEET 6 C10 SER C 174 PRO C 178 1 O ASN C 176 N LEU C 152 SHEET 7 C10 LYS C 203 TRP C 207 1 O VAL C 205 N VAL C 177 SHEET 8 C10 VAL C 229 ALA C 232 1 O VAL C 229 N LEU C 206 SHEET 9 C10 ILE C 8 HIS C 12 1 N ILE C 8 O VAL C 230 SHEET 10 C10 GLY C 37 LEU C 44 1 O GLU C 39 N GLY C 11 SHEET 1 D10 VAL D 50 VAL D 52 0 SHEET 2 D10 GLY D 37 LEU D 44 -1 N TRP D 43 O VAL D 51 SHEET 3 D10 LEU D 102 LEU D 107 1 O GLU D 106 N LEU D 40 SHEET 4 D10 VAL D 128 SER D 132 1 O SER D 131 N LEU D 107 SHEET 5 D10 THR D 149 LEU D 153 1 O THR D 149 N ILE D 130 SHEET 6 D10 SER D 174 PRO D 178 1 O ASN D 176 N LEU D 152 SHEET 7 D10 LYS D 203 TRP D 207 1 O VAL D 205 N VAL D 177 SHEET 8 D10 VAL D 229 ALA D 232 1 O VAL D 229 N LEU D 206 SHEET 9 D10 ILE D 8 HIS D 12 1 N ILE D 8 O VAL D 230 SHEET 10 D10 GLY D 37 LEU D 44 1 O GLY D 37 N GLY D 11 LINK OE2 GLU A 39 MG MG A 401 1555 1555 2.12 LINK OD1 ASP A 41 MG MG A 401 1555 1555 2.10 LINK OE1 GLU A 106 MG MG A 401 1555 1555 1.91 LINK MG MG A 401 O HOH A 713 1555 1555 1.95 LINK MG MG A 401 O HOH A 718 1555 1555 2.16 LINK OE2 GLU B 39 MG MG B 401 1555 1555 1.99 LINK OD1 ASP B 41 MG MG B 401 1555 1555 2.01 LINK OE1 GLU B 106 MG MG B 401 1555 1555 1.91 LINK MG MG B 401 O HOH B 530 1555 1555 2.19 LINK MG MG B 401 O HOH B 570 1555 1555 2.22 LINK OE2 GLU C 39 MG MG C 401 1555 1555 2.01 LINK OD1 ASP C 41 MG MG C 401 1555 1555 1.92 LINK OE2 GLU C 106 MG MG C 401 1555 1555 1.91 LINK MG MG C 401 O HOH C 592 1555 1555 2.12 LINK MG MG C 401 O HOH C 606 1555 1555 2.15 LINK OE2 GLU D 39 MG MG D 401 1555 1555 2.00 LINK OD1 ASP D 41 MG MG D 401 1555 1555 2.16 LINK OE1 GLU D 106 MG MG D 401 1555 1555 2.00 LINK MG MG D 401 O HOH D 666 1555 1555 1.98 LINK MG MG D 401 O HOH D 672 1555 1555 2.11 SITE 1 AC1 5 GLU A 39 ASP A 41 GLU A 106 HOH A 713 SITE 2 AC1 5 HOH A 718 SITE 1 AC2 5 GLU B 39 ASP B 41 GLU B 106 HOH B 530 SITE 2 AC2 5 HOH B 570 SITE 1 AC3 5 GLU C 39 ASP C 41 GLU C 106 HOH C 592 SITE 2 AC3 5 HOH C 606 SITE 1 AC4 5 GLU D 39 ASP D 41 GLU D 106 HOH D 666 SITE 2 AC4 5 HOH D 672 CRYST1 43.724 132.034 171.639 90.00 90.00 90.00 P 21 21 21 16 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 0.022871 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007574 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005826 0.00000