HEADER TRANSFERASE 06-OCT-09 3K56 TITLE CRYSTAL STRUCTURE OF ISOPENTENYL PHOSPHATE KINASE FROM M. JANNASCHII TITLE 2 IN COMPLEX WITH IPP BETA-S COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOPENTENYL PHOSPHATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII; SOURCE 3 ORGANISM_COMMON: METHANOCOCCUS JANNASCHII; SOURCE 4 ORGANISM_TAXID: 2190; SOURCE 5 GENE: MJ0044; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PHIS8 KEYWDS SMALL MOLECULE KINASE, ATP-BINDING, ATP GAMMA-S, TRANSFERASE, KEYWDS 2 METHANOCALDOCOCCUS JANNASCHII, ISOPENTENYL MONOPHOSPHATE, KEYWDS 3 ISOPENTENYL DIPHOSPHATE, ISOPRENOID BIOSYNTHESIS, MEVALONATE KEYWDS 4 PATHWAY, ARCHAEA EXPDTA X-RAY DIFFRACTION AUTHOR N.DELLAS,J.P.NOEL REVDAT 3 06-SEP-23 3K56 1 REMARK SEQADV REVDAT 2 07-JUL-10 3K56 1 JRNL REVDAT 1 05-MAY-10 3K56 0 JRNL AUTH N.DELLAS,J.P.NOEL JRNL TITL MUTATION OF ARCHAEAL ISOPENTENYL PHOSPHATE KINASE HIGHLIGHTS JRNL TITL 2 MECHANISM AND GUIDES PHOSPHORYLATION OF ADDITIONAL JRNL TITL 3 ISOPRENOID MONOPHOSPHATES. JRNL REF ACS CHEM.BIOL. V. 5 589 2010 JRNL REFN ISSN 1554-8929 JRNL PMID 20392112 JRNL DOI 10.1021/CB1000313 REMARK 2 REMARK 2 RESOLUTION. 2.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 29289 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1468 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) : 2.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.41 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1866 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.3280 REMARK 3 BIN FREE R VALUE SET COUNT : 106 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4075 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 68 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 57.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.78000 REMARK 3 B22 (A**2) : 1.59000 REMARK 3 B33 (A**2) : -2.36000 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): 0.325 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.240 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.196 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.419 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4203 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5660 ; 1.985 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 509 ; 6.817 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 185 ;36.819 ;25.135 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 812 ;18.499 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.276 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 625 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3058 ; 0.009 ; 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): 2534 ; 1.160 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4108 ; 2.108 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1669 ; 2.896 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1552 ; 4.630 ; 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 3K56 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055559. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29290 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.340 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.010 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.76 REMARK 200 R MERGE FOR SHELL (I) : 0.58300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 3K4O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M AMMONIUM SULFATE, 5MM ATP GAMMA REMARK 280 -S, 1MM IP, 2MM MAGNESIUM CHLORIDE., VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 38.84000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.12000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.84000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.12000 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: 4170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -67.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 -1.000000 0.000000 0.000000 77.68000 REMARK 350 BIOMT2 1 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11180 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -153.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 -1.000000 0.000000 0.000000 77.68000 REMARK 350 BIOMT2 1 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -5 REMARK 465 SER A -4 REMARK 465 HIS A -3 REMARK 465 GLY A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 GLY B -5 REMARK 465 SER B -4 REMARK 465 HIS B -3 REMARK 465 GLY B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 GLY B 208 REMARK 465 SER B 209 REMARK 465 ASN B 210 REMARK 465 SER B 211 REMARK 465 ILE B 212 REMARK 465 ASP B 213 REMARK 465 VAL B 214 REMARK 465 THR B 215 REMARK 465 GLY B 216 REMARK 465 GLY B 217 REMARK 465 SER B 259 REMARK 465 GLU B 260 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 N MET B 1 OD2 ASP B 173 1.92 REMARK 500 O HOH A 261 O HOH A 298 2.12 REMARK 500 N GLY B 159 O2 IS3 B 300 2.14 REMARK 500 OD1 ASP A 105 NZ LYS B 81 2.15 REMARK 500 O1 SO4 B 302 O HOH B 286 2.15 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 MET A 224 CG - SD - CE ANGL. DEV. = 10.6 DEGREES REMARK 500 PRO B 61 C - N - CA ANGL. DEV. = -12.2 DEGREES REMARK 500 ASP B 71 N - CA - C ANGL. DEV. = 22.0 DEGREES REMARK 500 ARG B 136 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 PRO B 190 C - N - CA ANGL. DEV. = 9.0 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 LEU A 7 -78.05 -82.56 REMARK 500 LEU A 7 -72.17 -82.56 REMARK 500 SER A 10 -79.85 -33.29 REMARK 500 SER A 13 132.72 -171.72 REMARK 500 LYS A 15 3.84 -62.82 REMARK 500 TYR A 19 17.20 50.92 REMARK 500 ASN A 44 59.19 36.47 REMARK 500 LYS A 73 164.62 174.32 REMARK 500 SER A 103 1.59 -68.12 REMARK 500 PHE A 116 -10.42 -151.02 REMARK 500 PHE A 125 84.91 -169.81 REMARK 500 ASN A 152 10.71 53.70 REMARK 500 LYS A 171 63.47 64.88 REMARK 500 ASP A 187 47.08 82.61 REMARK 500 LYS A 196 2.49 -61.60 REMARK 500 CYS A 230 -147.22 -124.07 REMARK 500 ASN A 241 -1.18 69.00 REMARK 500 GLU A 250 16.15 -149.78 REMARK 500 GLN B 43 10.15 -49.77 REMARK 500 ASN B 44 39.66 37.79 REMARK 500 ASP B 71 -24.65 -21.85 REMARK 500 LYS B 73 105.36 56.22 REMARK 500 LYS B 74 131.11 -31.57 REMARK 500 PHE B 116 -0.39 -160.09 REMARK 500 PHE B 119 -165.38 -79.55 REMARK 500 LYS B 122 103.41 56.23 REMARK 500 PHE B 125 88.62 -158.79 REMARK 500 ASP B 195 -158.68 -80.34 REMARK 500 LYS B 227 79.28 -65.69 REMARK 500 ASN B 228 -1.82 156.58 REMARK 500 ASN B 241 -11.39 88.11 REMARK 500 VAL B 251 141.82 -28.88 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 GLU B 70 ASP B 71 -114.53 REMARK 500 ASP B 71 GLY B 72 144.25 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 IS3 A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IS3 B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3K4O RELATED DB: PDB REMARK 900 IPK APO REMARK 900 RELATED ID: 3K4Y RELATED DB: PDB REMARK 900 IPK IN COMPLEX WITH IPP REMARK 900 RELATED ID: 3K52 RELATED DB: PDB REMARK 900 IPK IN COMPLEX WITH IP DBREF 3K56 A 1 260 UNP Q60352 Y044_METJA 1 260 DBREF 3K56 B 1 260 UNP Q60352 Y044_METJA 1 260 SEQADV 3K56 GLY A -5 UNP Q60352 EXPRESSION TAG SEQADV 3K56 SER A -4 UNP Q60352 EXPRESSION TAG SEQADV 3K56 HIS A -3 UNP Q60352 EXPRESSION TAG SEQADV 3K56 GLY A -2 UNP Q60352 EXPRESSION TAG SEQADV 3K56 GLY A -1 UNP Q60352 EXPRESSION TAG SEQADV 3K56 SER A 0 UNP Q60352 EXPRESSION TAG SEQADV 3K56 GLU A 223 UNP Q60352 ASP 223 CONFLICT SEQADV 3K56 GLY B -5 UNP Q60352 EXPRESSION TAG SEQADV 3K56 SER B -4 UNP Q60352 EXPRESSION TAG SEQADV 3K56 HIS B -3 UNP Q60352 EXPRESSION TAG SEQADV 3K56 GLY B -2 UNP Q60352 EXPRESSION TAG SEQADV 3K56 GLY B -1 UNP Q60352 EXPRESSION TAG SEQADV 3K56 SER B 0 UNP Q60352 EXPRESSION TAG SEQADV 3K56 GLU B 223 UNP Q60352 ASP 223 CONFLICT SEQRES 1 A 266 GLY SER HIS GLY GLY SER MET LEU THR ILE LEU LYS LEU SEQRES 2 A 266 GLY GLY SER ILE LEU SER ASP LYS ASN VAL PRO TYR SER SEQRES 3 A 266 ILE LYS TRP ASP ASN LEU GLU ARG ILE ALA MET GLU ILE SEQRES 4 A 266 LYS ASN ALA LEU ASP TYR TYR LYS ASN GLN ASN LYS GLU SEQRES 5 A 266 ILE LYS LEU ILE LEU VAL HIS GLY GLY GLY ALA PHE GLY SEQRES 6 A 266 HIS PRO VAL ALA LYS LYS TYR LEU LYS ILE GLU ASP GLY SEQRES 7 A 266 LYS LYS ILE PHE ILE ASN MET GLU LYS GLY PHE TRP GLU SEQRES 8 A 266 ILE GLN ARG ALA MET ARG ARG PHE ASN ASN ILE ILE ILE SEQRES 9 A 266 ASP THR LEU GLN SER TYR ASP ILE PRO ALA VAL SER ILE SEQRES 10 A 266 GLN PRO SER SER PHE VAL VAL PHE GLY ASP LYS LEU ILE SEQRES 11 A 266 PHE ASP THR SER ALA ILE LYS GLU MET LEU LYS ARG ASN SEQRES 12 A 266 LEU VAL PRO VAL ILE HIS GLY ASP ILE VAL ILE ASP ASP SEQRES 13 A 266 LYS ASN GLY TYR ARG ILE ILE SER GLY ASP ASP ILE VAL SEQRES 14 A 266 PRO TYR LEU ALA ASN GLU LEU LYS ALA ASP LEU ILE LEU SEQRES 15 A 266 TYR ALA THR ASP VAL ASP GLY VAL LEU ILE ASP ASN LYS SEQRES 16 A 266 PRO ILE LYS ARG ILE ASP LYS ASN ASN ILE TYR LYS ILE SEQRES 17 A 266 LEU ASN TYR LEU SER GLY SER ASN SER ILE ASP VAL THR SEQRES 18 A 266 GLY GLY MET LYS TYR LYS ILE GLU MET ILE ARG LYS ASN SEQRES 19 A 266 LYS CYS ARG GLY PHE VAL PHE ASN GLY ASN LYS ALA ASN SEQRES 20 A 266 ASN ILE TYR LYS ALA LEU LEU GLY GLU VAL GLU GLY THR SEQRES 21 A 266 GLU ILE ASP PHE SER GLU SEQRES 1 B 266 GLY SER HIS GLY GLY SER MET LEU THR ILE LEU LYS LEU SEQRES 2 B 266 GLY GLY SER ILE LEU SER ASP LYS ASN VAL PRO TYR SER SEQRES 3 B 266 ILE LYS TRP ASP ASN LEU GLU ARG ILE ALA MET GLU ILE SEQRES 4 B 266 LYS ASN ALA LEU ASP TYR TYR LYS ASN GLN ASN LYS GLU SEQRES 5 B 266 ILE LYS LEU ILE LEU VAL HIS GLY GLY GLY ALA PHE GLY SEQRES 6 B 266 HIS PRO VAL ALA LYS LYS TYR LEU LYS ILE GLU ASP GLY SEQRES 7 B 266 LYS LYS ILE PHE ILE ASN MET GLU LYS GLY PHE TRP GLU SEQRES 8 B 266 ILE GLN ARG ALA MET ARG ARG PHE ASN ASN ILE ILE ILE SEQRES 9 B 266 ASP THR LEU GLN SER TYR ASP ILE PRO ALA VAL SER ILE SEQRES 10 B 266 GLN PRO SER SER PHE VAL VAL PHE GLY ASP LYS LEU ILE SEQRES 11 B 266 PHE ASP THR SER ALA ILE LYS GLU MET LEU LYS ARG ASN SEQRES 12 B 266 LEU VAL PRO VAL ILE HIS GLY ASP ILE VAL ILE ASP ASP SEQRES 13 B 266 LYS ASN GLY TYR ARG ILE ILE SER GLY ASP ASP ILE VAL SEQRES 14 B 266 PRO TYR LEU ALA ASN GLU LEU LYS ALA ASP LEU ILE LEU SEQRES 15 B 266 TYR ALA THR ASP VAL ASP GLY VAL LEU ILE ASP ASN LYS SEQRES 16 B 266 PRO ILE LYS ARG ILE ASP LYS ASN ASN ILE TYR LYS ILE SEQRES 17 B 266 LEU ASN TYR LEU SER GLY SER ASN SER ILE ASP VAL THR SEQRES 18 B 266 GLY GLY MET LYS TYR LYS ILE GLU MET ILE ARG LYS ASN SEQRES 19 B 266 LYS CYS ARG GLY PHE VAL PHE ASN GLY ASN LYS ALA ASN SEQRES 20 B 266 ASN ILE TYR LYS ALA LEU LEU GLY GLU VAL GLU GLY THR SEQRES 21 B 266 GLU ILE ASP PHE SER GLU HET IS3 A 300 14 HET SO4 A 303 5 HET SO4 A 304 5 HET IS3 B 300 14 HET SO4 B 301 5 HET SO4 B 302 5 HETNAM IS3 ISOPENTENYL DIPHOSPHATE BETA-S HETNAM SO4 SULFATE ION HETSYN IS3 O-(3-METHYLBUTYL) TRIHYDROGEN THIODIPHOSPHATE FORMUL 3 IS3 2(C5 H14 O6 P2 S) FORMUL 4 SO4 4(O4 S 2-) FORMUL 9 HOH *68(H2 O) HELIX 1 1 GLY A 8 SER A 13 1 6 HELIX 2 2 LYS A 22 GLN A 43 1 22 HELIX 3 3 GLY A 55 LYS A 65 1 11 HELIX 4 4 ASN A 78 SER A 103 1 26 HELIX 5 5 GLN A 112 PHE A 116 5 5 HELIX 6 6 THR A 127 ARG A 136 1 10 HELIX 7 7 SER A 158 LYS A 171 1 14 HELIX 8 8 ASN A 198 GLY A 208 1 11 HELIX 9 9 GLY A 216 LYS A 229 1 14 HELIX 10 10 ASN A 241 LEU A 248 1 8 HELIX 11 11 GLY B 8 SER B 13 1 6 HELIX 12 12 LYS B 22 GLN B 43 1 22 HELIX 13 13 GLY B 55 LYS B 65 1 11 HELIX 14 14 ASN B 78 TYR B 104 1 27 HELIX 15 15 GLN B 112 PHE B 116 5 5 HELIX 16 16 THR B 127 ARG B 136 1 10 HELIX 17 17 SER B 158 LEU B 170 1 13 HELIX 18 18 ASN B 197 LEU B 206 1 10 HELIX 19 19 MET B 218 LYS B 227 1 10 HELIX 20 20 ASN B 241 LEU B 248 1 8 SHEET 1 A 8 ALA A 108 ILE A 111 0 SHEET 2 A 8 VAL A 139 HIS A 143 1 O VAL A 141 N ILE A 111 SHEET 3 A 8 LYS A 48 HIS A 53 1 N LEU A 51 O ILE A 142 SHEET 4 A 8 LEU A 2 LYS A 6 1 N THR A 3 O LYS A 48 SHEET 5 A 8 LEU A 174 THR A 179 1 O LEU A 176 N LYS A 6 SHEET 6 A 8 ARG A 231 ASN A 236 1 O PHE A 233 N TYR A 177 SHEET 7 A 8 THR A 254 ASP A 257 -1 O ILE A 256 N GLY A 232 SHEET 8 A 8 ARG A 193 ILE A 194 1 N ILE A 194 O ASP A 257 SHEET 1 B 2 LEU A 67 ILE A 69 0 SHEET 2 B 2 LYS A 74 PHE A 76 -1 O ILE A 75 N LYS A 68 SHEET 1 C 2 VAL A 118 PHE A 119 0 SHEET 2 C 2 LEU A 123 ILE A 124 -1 O ILE A 124 N VAL A 118 SHEET 1 D 2 ASP A 145 ILE A 148 0 SHEET 2 D 2 TYR A 154 ILE A 157 -1 O ARG A 155 N VAL A 147 SHEET 1 E 7 ALA B 108 ILE B 111 0 SHEET 2 E 7 VAL B 139 HIS B 143 1 O VAL B 141 N VAL B 109 SHEET 3 E 7 LYS B 48 HIS B 53 1 N LEU B 51 O PRO B 140 SHEET 4 E 7 LEU B 2 LEU B 7 1 N LEU B 7 O VAL B 52 SHEET 5 E 7 LEU B 174 THR B 179 1 O LEU B 176 N LYS B 6 SHEET 6 E 7 ARG B 231 ASN B 236 1 O PHE B 233 N TYR B 177 SHEET 7 E 7 THR B 254 ASP B 257 -1 O THR B 254 N VAL B 234 SHEET 1 F 2 LEU B 67 ILE B 69 0 SHEET 2 F 2 LYS B 74 PHE B 76 -1 O ILE B 75 N LYS B 68 SHEET 1 G 3 VAL B 118 PHE B 119 0 SHEET 2 G 3 ASP B 145 ASP B 149 1 O ILE B 148 N PHE B 119 SHEET 3 G 3 GLY B 153 ILE B 157 -1 O GLY B 153 N ASP B 149 SITE 1 AC1 11 LYS A 6 GLY A 9 GLY A 54 GLY A 55 SITE 2 AC1 11 GLY A 56 GLY A 59 HIS A 60 GLY A 144 SITE 3 AC1 11 ILE A 156 SER A 158 GLY A 159 SITE 1 AC2 3 LYS A 6 GLY A 9 LYS A 221 SITE 1 AC3 7 ILE A 21 LYS A 22 TRP A 23 ASP A 24 SITE 2 AC3 7 ARG A 88 HOH A 279 HOH A 286 SITE 1 AC4 9 GLY B 9 GLY B 54 GLY B 55 GLY B 56 SITE 2 AC4 9 GLY B 59 HIS B 60 GLY B 144 SER B 158 SITE 3 AC4 9 GLY B 159 SITE 1 AC5 5 LYS B 6 GLY B 8 SER B 10 THR B 179 SITE 2 AC5 5 HOH B 288 SITE 1 AC6 4 LYS B 22 TRP B 23 ASP B 24 HOH B 286 CRYST1 77.680 100.240 87.790 90.00 90.00 90.00 P 21 21 2 8 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 0.012873 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009976 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011391 0.00000