HEADER LIGASE 19-AUG-13 4MB2 TITLE CRYSTAL STRUCTURE OF TON1374 IN COMPLEX WITH ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOPANTOTHENATE SYNTHETASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 5 EC: 6.3.2.26; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOCOCCUS ONNURINEUS; SOURCE 3 ORGANISM_TAXID: 523850; SOURCE 4 STRAIN: NA1; SOURCE 5 GENE: TON_1374; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIGASE, ATP BINDING EXPDTA X-RAY DIFFRACTION AUTHOR M.-K.KIM,Y.J.AN,S.-S.CHA REVDAT 2 20-MAR-24 4MB2 1 REMARK REVDAT 1 06-AUG-14 4MB2 0 JRNL AUTH M.-K.KIM,Y.J.AN,S.-S.CHA JRNL TITL THE CRYSTAL STRUCTURE OF A NOVEL PHOSPHOPANTOTHENATE JRNL TITL 2 SYNTHETASE FROM THE HYPERTHERMOPHILIC ARCHAEA, THERMOCOCCUS JRNL TITL 3 ONNURINEUS NA1 JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 439 533 2013 JRNL REFN ISSN 0006-291X JRNL PMID 24021277 JRNL DOI 10.1016/J.BBRC.2013.09.008 REMARK 2 REMARK 2 RESOLUTION. 2.19 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 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) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 57833 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3084 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) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4073 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE SET COUNT : 219 REMARK 3 BIN FREE R VALUE : 0.3720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8021 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 125 REMARK 3 SOLVENT ATOMS : 179 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : 0.59000 REMARK 3 B33 (A**2) : -1.06000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.67000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.264 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.222 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.180 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.318 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.921 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8270 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 8245 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11184 ; 1.083 ; 2.007 REMARK 3 BOND ANGLES OTHERS (DEGREES): 18918 ; 0.567 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1003 ; 7.939 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 371 ;37.186 ;23.154 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1549 ;20.922 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 92 ;22.805 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1264 ; 0.067 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9054 ; 0.015 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1766 ; 0.002 ; 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 : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4MB2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1000081690. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-MAY-13 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60918 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.08M TRIS-HCL, 24%(W/V) POLYETHYLENE REMARK 280 GLYCOL 4000, 4MM ATP, PH 8.5, VAPOR DIFFUSION, TEMPERATURE 295K 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 133.21400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.45450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 133.21400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.45450 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 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 1 REMARK 465 VAL A 2 REMARK 465 LYS A 3 REMARK 465 ILE A 4 REMARK 465 PRO A 5 REMARK 465 LYS A 6 REMARK 465 SER A 7 REMARK 465 HIS A 8 REMARK 465 ASP A 261 REMARK 465 MET B 1 REMARK 465 GLN B 259 REMARK 465 LEU B 260 REMARK 465 ASP B 261 REMARK 465 MET C 1 REMARK 465 VAL C 2 REMARK 465 LYS C 3 REMARK 465 ILE C 4 REMARK 465 PRO C 5 REMARK 465 LYS C 6 REMARK 465 SER C 7 REMARK 465 HIS C 8 REMARK 465 LEU C 139 REMARK 465 GLU C 140 REMARK 465 HIS C 141 REMARK 465 GLU C 142 REMARK 465 ARG C 143 REMARK 465 LEU C 260 REMARK 465 ASP C 261 REMARK 465 MET D 1 REMARK 465 VAL D 2 REMARK 465 LYS D 3 REMARK 465 ILE D 4 REMARK 465 PRO D 5 REMARK 465 LYS D 6 REMARK 465 ARG D 143 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 ARG A 143 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 124 CG CD OE1 OE2 REMARK 470 HIS B 141 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B 143 CG CD NE CZ NH1 NH2 REMARK 470 SER D 7 OG REMARK 470 HIS D 8 CG ND1 CD2 CE1 NE2 REMARK 470 HIS D 141 CG ND1 CD2 CE1 NE2 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 NH2 ARG B 106 O GLY B 129 1.81 REMARK 500 NH1 ARG A 256 O MET B 191 1.93 REMARK 500 O HOH B 451 O HOH B 457 1.98 REMARK 500 OD1 ASN B 102 NH1 ARG B 166 2.03 REMARK 500 OE1 GLN A 259 NZ LYS C 31 2.03 REMARK 500 NH1 ARG C 256 O MET D 191 2.04 REMARK 500 O GLU B 140 N GLU B 142 2.10 REMARK 500 O VAL C 159 OG1 THR C 179 2.19 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 B 450 O HOH C 435 4545 1.74 REMARK 500 O HOH B 444 O HOH C 403 4545 1.81 REMARK 500 O HOH A 443 O HOH B 447 2555 1.86 REMARK 500 O LEU A 139 O LEU A 139 2555 2.08 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 ASN A 71 50.81 -142.59 REMARK 500 VAL A 84 46.07 -142.47 REMARK 500 ASP A 122 93.78 -166.64 REMARK 500 LEU A 139 -143.53 -118.54 REMARK 500 ASP B 122 88.25 -160.97 REMARK 500 LEU B 139 -135.69 72.35 REMARK 500 HIS B 141 71.33 -27.53 REMARK 500 GLU B 142 10.50 51.74 REMARK 500 ARG B 143 1.43 -67.88 REMARK 500 ASP B 181 118.21 -164.44 REMARK 500 ARG B 256 79.41 47.03 REMARK 500 LYS B 257 -51.58 172.33 REMARK 500 ALA C 30 158.49 -48.86 REMARK 500 PHE C 104 -93.04 -101.84 REMARK 500 TYR C 105 94.96 -67.97 REMARK 500 ARG D 10 44.77 -78.11 REMARK 500 VAL D 84 52.78 -143.41 REMARK 500 GLU D 124 -135.36 -82.66 REMARK 500 ILE D 125 119.41 73.71 REMARK 500 LEU D 139 127.47 79.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 9 ARG A 10 118.22 REMARK 500 LEU C 103 PHE C 104 -138.87 REMARK 500 GLY D 129 ILE D 130 147.83 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 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 301 O1B REMARK 620 2 ATP A 301 O3G 65.4 REMARK 620 3 ATP A 301 O1A 75.4 63.0 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP D 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MB0 RELATED DB: PDB DBREF 4MB2 A 1 261 UNP B6YXQ1 B6YXQ1_THEON 1 261 DBREF 4MB2 B 1 261 UNP B6YXQ1 B6YXQ1_THEON 1 261 DBREF 4MB2 C 1 261 UNP B6YXQ1 B6YXQ1_THEON 1 261 DBREF 4MB2 D 1 261 UNP B6YXQ1 B6YXQ1_THEON 1 261 SEQRES 1 A 261 MET VAL LYS ILE PRO LYS SER HIS PRO ARG TYR TRP SER SEQRES 2 A 261 LEU TYR TYR ARG GLU LYS ILE ILE GLU GLY MET GLU LYS SEQRES 3 A 261 GLY MET THR ALA LYS ALA GLY LEU ILE ALA HIS GLY ARG SEQRES 4 A 261 GLY GLU ALA PHE ASP TYR LEU ILE GLY GLU ARG THR ILE SEQRES 5 A 261 GLU PRO ALA GLU ARG ALA MET ARG ALA ALA VAL ALA LYS SEQRES 6 A 261 LEU LEU LEU ALA GLU ASN PRO VAL VAL SER VAL ASN GLY SEQRES 7 A 261 ASN VAL ALA ALA LEU VAL PRO LYS GLU THR ILE GLU LEU SEQRES 8 A 261 ALA ARG ALA LEU ASN ALA LYS LEU GLU ILE ASN LEU PHE SEQRES 9 A 261 TYR ARG THR GLU ASP ARG VAL LYS ALA ILE ALA GLU GLU SEQRES 10 A 261 LEU ARG LYS TYR ASP PRO GLU ILE GLU LEU LEU GLY ILE SEQRES 11 A 261 ASN PRO THR LYS ARG ILE PRO GLY LEU GLU HIS GLU ARG SEQRES 12 A 261 GLY LYS VAL ASP GLU ASN GLY ILE TRP LYS ALA ASP VAL SEQRES 13 A 261 VAL VAL VAL PRO LEU GLU ASP GLY ASP ARG THR GLU ALA SEQRES 14 A 261 LEU VAL ARG MET GLY LYS PHE VAL ILE THR ILE ASP LEU SEQRES 15 A 261 ASN PRO LEU SER ARG SER ALA ARG MET ALA ASP ILE THR SEQRES 16 A 261 ILE VAL ASP ASN ILE VAL ARG ALA TYR PRO ARG MET THR SEQRES 17 A 261 GLU LEU ALA ARG GLU MET LYS ASP TYR SER ARG GLY GLU SEQRES 18 A 261 LEU ILE ARG ILE ILE GLU GLU TYR ASP ASN GLY LYS THR SEQRES 19 A 261 LEU ASN ASP VAL LEU LEU HIS ILE ARG ASP ARG LEU THR SEQRES 20 A 261 LYS LEU ALA GLU GLY GLY ILE TRP ARG LYS LYS GLN LEU SEQRES 21 A 261 ASP SEQRES 1 B 261 MET VAL LYS ILE PRO LYS SER HIS PRO ARG TYR TRP SER SEQRES 2 B 261 LEU TYR TYR ARG GLU LYS ILE ILE GLU GLY MET GLU LYS SEQRES 3 B 261 GLY MET THR ALA LYS ALA GLY LEU ILE ALA HIS GLY ARG SEQRES 4 B 261 GLY GLU ALA PHE ASP TYR LEU ILE GLY GLU ARG THR ILE SEQRES 5 B 261 GLU PRO ALA GLU ARG ALA MET ARG ALA ALA VAL ALA LYS SEQRES 6 B 261 LEU LEU LEU ALA GLU ASN PRO VAL VAL SER VAL ASN GLY SEQRES 7 B 261 ASN VAL ALA ALA LEU VAL PRO LYS GLU THR ILE GLU LEU SEQRES 8 B 261 ALA ARG ALA LEU ASN ALA LYS LEU GLU ILE ASN LEU PHE SEQRES 9 B 261 TYR ARG THR GLU ASP ARG VAL LYS ALA ILE ALA GLU GLU SEQRES 10 B 261 LEU ARG LYS TYR ASP PRO GLU ILE GLU LEU LEU GLY ILE SEQRES 11 B 261 ASN PRO THR LYS ARG ILE PRO GLY LEU GLU HIS GLU ARG SEQRES 12 B 261 GLY LYS VAL ASP GLU ASN GLY ILE TRP LYS ALA ASP VAL SEQRES 13 B 261 VAL VAL VAL PRO LEU GLU ASP GLY ASP ARG THR GLU ALA SEQRES 14 B 261 LEU VAL ARG MET GLY LYS PHE VAL ILE THR ILE ASP LEU SEQRES 15 B 261 ASN PRO LEU SER ARG SER ALA ARG MET ALA ASP ILE THR SEQRES 16 B 261 ILE VAL ASP ASN ILE VAL ARG ALA TYR PRO ARG MET THR SEQRES 17 B 261 GLU LEU ALA ARG GLU MET LYS ASP TYR SER ARG GLY GLU SEQRES 18 B 261 LEU ILE ARG ILE ILE GLU GLU TYR ASP ASN GLY LYS THR SEQRES 19 B 261 LEU ASN ASP VAL LEU LEU HIS ILE ARG ASP ARG LEU THR SEQRES 20 B 261 LYS LEU ALA GLU GLY GLY ILE TRP ARG LYS LYS GLN LEU SEQRES 21 B 261 ASP SEQRES 1 C 261 MET VAL LYS ILE PRO LYS SER HIS PRO ARG TYR TRP SER SEQRES 2 C 261 LEU TYR TYR ARG GLU LYS ILE ILE GLU GLY MET GLU LYS SEQRES 3 C 261 GLY MET THR ALA LYS ALA GLY LEU ILE ALA HIS GLY ARG SEQRES 4 C 261 GLY GLU ALA PHE ASP TYR LEU ILE GLY GLU ARG THR ILE SEQRES 5 C 261 GLU PRO ALA GLU ARG ALA MET ARG ALA ALA VAL ALA LYS SEQRES 6 C 261 LEU LEU LEU ALA GLU ASN PRO VAL VAL SER VAL ASN GLY SEQRES 7 C 261 ASN VAL ALA ALA LEU VAL PRO LYS GLU THR ILE GLU LEU SEQRES 8 C 261 ALA ARG ALA LEU ASN ALA LYS LEU GLU ILE ASN LEU PHE SEQRES 9 C 261 TYR ARG THR GLU ASP ARG VAL LYS ALA ILE ALA GLU GLU SEQRES 10 C 261 LEU ARG LYS TYR ASP PRO GLU ILE GLU LEU LEU GLY ILE SEQRES 11 C 261 ASN PRO THR LYS ARG ILE PRO GLY LEU GLU HIS GLU ARG SEQRES 12 C 261 GLY LYS VAL ASP GLU ASN GLY ILE TRP LYS ALA ASP VAL SEQRES 13 C 261 VAL VAL VAL PRO LEU GLU ASP GLY ASP ARG THR GLU ALA SEQRES 14 C 261 LEU VAL ARG MET GLY LYS PHE VAL ILE THR ILE ASP LEU SEQRES 15 C 261 ASN PRO LEU SER ARG SER ALA ARG MET ALA ASP ILE THR SEQRES 16 C 261 ILE VAL ASP ASN ILE VAL ARG ALA TYR PRO ARG MET THR SEQRES 17 C 261 GLU LEU ALA ARG GLU MET LYS ASP TYR SER ARG GLY GLU SEQRES 18 C 261 LEU ILE ARG ILE ILE GLU GLU TYR ASP ASN GLY LYS THR SEQRES 19 C 261 LEU ASN ASP VAL LEU LEU HIS ILE ARG ASP ARG LEU THR SEQRES 20 C 261 LYS LEU ALA GLU GLY GLY ILE TRP ARG LYS LYS GLN LEU SEQRES 21 C 261 ASP SEQRES 1 D 261 MET VAL LYS ILE PRO LYS SER HIS PRO ARG TYR TRP SER SEQRES 2 D 261 LEU TYR TYR ARG GLU LYS ILE ILE GLU GLY MET GLU LYS SEQRES 3 D 261 GLY MET THR ALA LYS ALA GLY LEU ILE ALA HIS GLY ARG SEQRES 4 D 261 GLY GLU ALA PHE ASP TYR LEU ILE GLY GLU ARG THR ILE SEQRES 5 D 261 GLU PRO ALA GLU ARG ALA MET ARG ALA ALA VAL ALA LYS SEQRES 6 D 261 LEU LEU LEU ALA GLU ASN PRO VAL VAL SER VAL ASN GLY SEQRES 7 D 261 ASN VAL ALA ALA LEU VAL PRO LYS GLU THR ILE GLU LEU SEQRES 8 D 261 ALA ARG ALA LEU ASN ALA LYS LEU GLU ILE ASN LEU PHE SEQRES 9 D 261 TYR ARG THR GLU ASP ARG VAL LYS ALA ILE ALA GLU GLU SEQRES 10 D 261 LEU ARG LYS TYR ASP PRO GLU ILE GLU LEU LEU GLY ILE SEQRES 11 D 261 ASN PRO THR LYS ARG ILE PRO GLY LEU GLU HIS GLU ARG SEQRES 12 D 261 GLY LYS VAL ASP GLU ASN GLY ILE TRP LYS ALA ASP VAL SEQRES 13 D 261 VAL VAL VAL PRO LEU GLU ASP GLY ASP ARG THR GLU ALA SEQRES 14 D 261 LEU VAL ARG MET GLY LYS PHE VAL ILE THR ILE ASP LEU SEQRES 15 D 261 ASN PRO LEU SER ARG SER ALA ARG MET ALA ASP ILE THR SEQRES 16 D 261 ILE VAL ASP ASN ILE VAL ARG ALA TYR PRO ARG MET THR SEQRES 17 D 261 GLU LEU ALA ARG GLU MET LYS ASP TYR SER ARG GLY GLU SEQRES 18 D 261 LEU ILE ARG ILE ILE GLU GLU TYR ASP ASN GLY LYS THR SEQRES 19 D 261 LEU ASN ASP VAL LEU LEU HIS ILE ARG ASP ARG LEU THR SEQRES 20 D 261 LYS LEU ALA GLU GLY GLY ILE TRP ARG LYS LYS GLN LEU SEQRES 21 D 261 ASP HET ATP A 301 31 HET MG A 302 1 HET ATP B 301 31 HET ATP C 301 31 HET ATP D 301 31 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 5 ATP 4(C10 H16 N5 O13 P3) FORMUL 6 MG MG 2+ FORMUL 10 HOH *179(H2 O) HELIX 1 1 ARG A 10 LYS A 26 1 17 HELIX 2 2 ALA A 30 GLY A 48 1 19 HELIX 3 3 ILE A 52 ALA A 69 1 18 HELIX 4 4 ASN A 77 VAL A 84 1 8 HELIX 5 5 VAL A 84 ASN A 96 1 13 HELIX 6 6 THR A 107 ASP A 122 1 16 HELIX 7 7 GLY A 150 ALA A 154 5 5 HELIX 8 8 ASP A 163 MET A 173 1 11 HELIX 9 9 SER A 186 ALA A 192 1 7 HELIX 10 10 ASN A 199 LYS A 215 1 17 HELIX 11 11 SER A 218 TYR A 229 1 12 HELIX 12 12 ASP A 230 GLY A 253 1 24 HELIX 13 13 ARG B 10 LYS B 26 1 17 HELIX 14 14 ALA B 30 GLY B 48 1 19 HELIX 15 15 ILE B 52 LEU B 68 1 17 HELIX 16 16 ASN B 77 VAL B 84 1 8 HELIX 17 17 VAL B 84 ASN B 96 1 13 HELIX 18 18 THR B 107 LYS B 120 1 14 HELIX 19 19 ASP B 163 GLY B 174 1 12 HELIX 20 20 SER B 186 ALA B 192 1 7 HELIX 21 21 ASN B 199 LYS B 215 1 17 HELIX 22 22 SER B 218 TYR B 229 1 12 HELIX 23 23 ASP B 230 GLU B 251 1 22 HELIX 24 24 ARG C 10 LYS C 26 1 17 HELIX 25 25 ALA C 30 GLY C 48 1 19 HELIX 26 26 ILE C 52 LEU C 68 1 17 HELIX 27 27 ASN C 77 VAL C 84 1 8 HELIX 28 28 VAL C 84 LEU C 95 1 12 HELIX 29 29 THR C 107 LYS C 120 1 14 HELIX 30 30 ASP C 163 GLY C 174 1 12 HELIX 31 31 SER C 186 ALA C 192 1 7 HELIX 32 32 ASN C 199 LYS C 215 1 17 HELIX 33 33 SER C 218 TYR C 229 1 12 HELIX 34 34 ASP C 230 GLY C 253 1 24 HELIX 35 35 ARG D 10 LYS D 26 1 17 HELIX 36 36 ALA D 30 GLY D 48 1 19 HELIX 37 37 ILE D 52 LEU D 68 1 17 HELIX 38 38 ASN D 77 VAL D 84 1 8 HELIX 39 39 VAL D 84 LEU D 95 1 12 HELIX 40 40 THR D 107 ASP D 122 1 16 HELIX 41 41 ASP D 163 GLY D 174 1 12 HELIX 42 42 SER D 186 ALA D 192 1 7 HELIX 43 43 ASN D 199 MET D 214 1 16 HELIX 44 44 LYS D 215 TYR D 217 5 3 HELIX 45 45 SER D 218 TYR D 229 1 12 HELIX 46 46 ASP D 230 GLU D 251 1 22 SHEET 1 A 6 LEU A 127 LEU A 128 0 SHEET 2 A 6 LYS A 98 ILE A 101 1 N LEU A 99 O LEU A 128 SHEET 3 A 6 VAL A 73 VAL A 76 1 N VAL A 76 O GLU A 100 SHEET 4 A 6 VAL A 156 VAL A 158 1 O VAL A 158 N SER A 75 SHEET 5 A 6 PHE A 176 ILE A 180 1 O ILE A 178 N VAL A 157 SHEET 6 A 6 ILE A 194 ILE A 196 1 O ILE A 196 N THR A 179 SHEET 1 B 2 LYS A 134 ARG A 135 0 SHEET 2 B 2 LYS A 145 VAL A 146 -1 O VAL A 146 N LYS A 134 SHEET 1 C 6 LEU B 127 LEU B 128 0 SHEET 2 C 6 LYS B 98 ILE B 101 1 N LEU B 99 O LEU B 128 SHEET 3 C 6 VAL B 73 VAL B 76 1 N VAL B 74 O LYS B 98 SHEET 4 C 6 VAL B 156 VAL B 158 1 O VAL B 158 N SER B 75 SHEET 5 C 6 PHE B 176 ILE B 180 1 O ILE B 178 N VAL B 157 SHEET 6 C 6 ILE B 194 ILE B 196 1 O ILE B 196 N THR B 179 SHEET 1 D 6 LEU C 127 LEU C 128 0 SHEET 2 D 6 LYS C 98 ILE C 101 1 N LEU C 99 O LEU C 128 SHEET 3 D 6 PRO C 72 VAL C 76 1 N VAL C 74 O LYS C 98 SHEET 4 D 6 VAL C 156 VAL C 158 1 O VAL C 158 N SER C 75 SHEET 5 D 6 PHE C 176 ILE C 180 1 O ILE C 178 N VAL C 157 SHEET 6 D 6 ILE C 194 ILE C 196 1 O ILE C 196 N THR C 179 SHEET 1 E 2 LYS C 134 ARG C 135 0 SHEET 2 E 2 LYS C 145 VAL C 146 -1 O VAL C 146 N LYS C 134 SHEET 1 F 6 LEU D 127 LEU D 128 0 SHEET 2 F 6 LYS D 98 ILE D 101 1 N ILE D 101 O LEU D 128 SHEET 3 F 6 VAL D 73 VAL D 76 1 N VAL D 74 O GLU D 100 SHEET 4 F 6 VAL D 156 VAL D 158 1 O VAL D 158 N VAL D 73 SHEET 5 F 6 PHE D 176 ILE D 180 1 O ILE D 178 N VAL D 157 SHEET 6 F 6 ILE D 194 ILE D 196 1 O ILE D 196 N THR D 179 SHEET 1 G 2 LYS D 134 ARG D 135 0 SHEET 2 G 2 LYS D 145 VAL D 146 -1 O VAL D 146 N LYS D 134 LINK O1B ATP A 301 MG MG A 302 1555 1555 2.25 LINK O3G ATP A 301 MG MG A 302 1555 1555 2.52 LINK O1A ATP A 301 MG MG A 302 1555 1555 2.83 CISPEP 1 ARG B 256 LYS B 257 0 13.80 CISPEP 2 HIS D 141 GLU D 142 0 21.41 SITE 1 AC1 15 ALA A 36 ARG A 39 GLY A 40 LEU A 161 SITE 2 AC1 15 ASP A 163 ASP A 181 LEU A 182 ASN A 183 SITE 3 AC1 15 ASP A 198 ASN A 199 ILE A 200 MG A 302 SITE 4 AC1 15 HOH A 404 HOH A 405 ARG B 17 SITE 1 AC2 1 ATP A 301 SITE 1 AC3 16 ARG A 17 TYR A 45 ALA B 36 ARG B 39 SITE 2 AC3 16 LEU B 161 GLU B 162 ASP B 163 GLY B 164 SITE 3 AC3 16 ASP B 181 LEU B 182 ARG B 187 SER B 188 SITE 4 AC3 16 ASP B 198 ASN B 199 ILE B 200 HOH B 425 SITE 1 AC4 12 ALA C 36 ARG C 39 GLY C 40 LEU C 161 SITE 2 AC4 12 ASP C 181 LEU C 182 ASP C 198 ASN C 199 SITE 3 AC4 12 ILE C 200 HOH C 419 ARG D 10 ARG D 17 SITE 1 AC5 14 ARG C 17 TYR C 45 ALA D 36 ARG D 39 SITE 2 AC5 14 LEU D 161 GLU D 162 ASP D 163 ASP D 181 SITE 3 AC5 14 LEU D 182 ASN D 183 SER D 186 ASP D 198 SITE 4 AC5 14 ASN D 199 ILE D 200 CRYST1 266.428 60.909 75.241 90.00 92.38 90.00 C 1 2 1 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 0.003753 0.000000 0.000156 0.00000 SCALE2 0.000000 0.016418 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013302 0.00000