HEADER TRANSFERASE 12-OCT-04 1XQI TITLE CRYSTAL STRUCTURE ANALYSIS OF AN NDP KINASE FROM PYROBACULUM TITLE 2 AEROPHILUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOSIDE DIPHOSPHATE KINASE; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: NDK, NDP KINASE, NUCLEOSIDE-2-P KINASE; COMPND 5 EC: 2.7.4.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROBACULUM AEROPHILUM; SOURCE 3 ORGANISM_TAXID: 13773; SOURCE 4 STRAIN: STRAIN IM2 DSM 7523 ATCC 51768; SOURCE 5 GENE: NDK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); 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: MODIFIED PET 28 C-6HIS KEYWDS ALPHA/BETA SANDWICH, FERREDOXIN FOLD, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.D.PEDELACQ,G.S.WALDO,S.CABANTOUS,E.C.LIONG,J.BERENDZEN, AUTHOR 2 T.C.TERWILLIGER REVDAT 4 20-OCT-21 1XQI 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1XQI 1 VERSN REVDAT 2 18-OCT-05 1XQI 1 JRNL REVDAT 1 20-SEP-05 1XQI 0 JRNL AUTH J.D.PEDELACQ,G.S.WALDO,S.CABANTOUS,E.C.LIONG,T.C.TERWILLIGER JRNL TITL STRUCTURAL AND FUNCTIONAL FEATURES OF AN NDP KINASE FROM THE JRNL TITL 2 HYPERTHERMOPHILE CRENARCHAEON PYROBACULUM AEROPHILUM JRNL REF PROTEIN SCI. V. 14 2562 2005 JRNL REFN ISSN 0961-8368 JRNL PMID 16195547 JRNL DOI 10.1110/PS.051664205 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 20785 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) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1620 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1568 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 126 REMARK 3 BIN FREE R VALUE : 0.3060 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4242 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.64000 REMARK 3 B22 (A**2) : 0.62000 REMARK 3 B33 (A**2) : -1.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.82000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.594 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.313 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.208 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.260 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.886 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4365 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5897 ; 1.886 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 543 ; 6.445 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;40.963 ;23.575 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 744 ;20.308 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;24.981 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 669 ; 0.115 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3211 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2020 ; 0.242 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2949 ; 0.315 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 206 ; 0.176 ; 0.200 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): 117 ; 0.244 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 26 ; 0.214 ; 0.200 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): 2821 ; 0.948 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4421 ; 1.596 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1733 ; 2.549 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1476 ; 4.150 ; 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 : BABINET MODEL WITH 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: NULL REMARK 4 REMARK 4 1XQI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000030648. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-00 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 : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792, 0.9791, 0.9500 REMARK 200 MONOCHROMATOR : SI 111 DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22330 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, PH 8.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 298K 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 62.51100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.02050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 62.51100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.02050 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 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: 2960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC 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 BIOMT1 2 -1.000000 0.000000 0.000000 53.01587 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 76.41105 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 -62.51100 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 -36.02050 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -9.49513 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -36.02050 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 76.41105 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 -72.00613 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 76.41105 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 MSE A 1 REMARK 465 HIS A 2 REMARK 465 ALA A 3 REMARK 465 ILE A 4 REMARK 465 ASN A 5 REMARK 465 ILE A 6 REMARK 465 ALA A 7 REMARK 465 PHE A 8 REMARK 465 PHE A 9 REMARK 465 ASP A 10 REMARK 465 LEU A 11 REMARK 465 ILE A 12 REMARK 465 MSE A 13 REMARK 465 MSE B 1 REMARK 465 HIS B 2 REMARK 465 ALA B 3 REMARK 465 ILE B 4 REMARK 465 ASN B 5 REMARK 465 ILE B 6 REMARK 465 ALA B 7 REMARK 465 PHE B 8 REMARK 465 PHE B 9 REMARK 465 ASP B 10 REMARK 465 LEU B 11 REMARK 465 ILE B 12 REMARK 465 MSE B 13 REMARK 465 MSE C 1 REMARK 465 HIS C 2 REMARK 465 ALA C 3 REMARK 465 ILE C 4 REMARK 465 ASN C 5 REMARK 465 ILE C 6 REMARK 465 ALA C 7 REMARK 465 PHE C 8 REMARK 465 PHE C 9 REMARK 465 ASP C 10 REMARK 465 LEU C 11 REMARK 465 ILE C 12 REMARK 465 MSE C 13 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 LYS A 79 CG CD CE NZ REMARK 470 GLU A 181 CG CD OE1 OE2 REMARK 470 LYS B 45 CG CD CE NZ REMARK 470 LYS B 79 CG CD CE NZ REMARK 470 GLU B 181 CG CD OE1 OE2 REMARK 470 LYS C 45 CG CD CE NZ REMARK 470 LYS C 79 CG CD CE NZ REMARK 470 GLU C 181 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OD2 ASP A 25 OH TYR A 111 2.16 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 NH2 ARG B 89 OD2 ASP B 95 2757 2.12 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 25 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 38 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 149 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 149 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 LEU B 22 CB - CG - CD2 ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG B 89 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 MSE C 51 CG - SE - CE ANGL. DEV. = -15.7 DEGREES REMARK 500 ARG C 149 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG C 149 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG C 185 NE - CZ - NH2 ANGL. DEV. = 3.8 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 170 -45.82 77.16 REMARK 500 LEU B 170 -38.35 77.87 REMARK 500 LEU C 170 -42.45 76.78 REMARK 500 GLU C 191 56.27 -95.28 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 TRS A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS C 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE B 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PGE C 700 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NPK RELATED DB: PDB REMARK 900 THE SAME PROTEIN FROM DICTYOSTELIUM DISCOIDEUM DBREF 1XQI A 1 195 UNP Q8ZWY4 NDK_PYRAE 1 195 DBREF 1XQI B 1 195 UNP Q8ZWY4 NDK_PYRAE 1 195 DBREF 1XQI C 1 195 UNP Q8ZWY4 NDK_PYRAE 1 195 SEQADV 1XQI MSE A 1 UNP Q8ZWY4 MET 1 MODIFIED RESIDUE SEQADV 1XQI ASP A 10 UNP Q8ZWY4 ALA 10 ENGINEERED MUTATION SEQADV 1XQI MSE A 13 UNP Q8ZWY4 MET 13 MODIFIED RESIDUE SEQADV 1XQI ASP A 33 UNP Q8ZWY4 GLY 33 ENGINEERED MUTATION SEQADV 1XQI LYS A 40 UNP Q8ZWY4 GLU 40 ENGINEERED MUTATION SEQADV 1XQI MSE A 51 UNP Q8ZWY4 MET 51 MODIFIED RESIDUE SEQADV 1XQI GLN A 71 UNP Q8ZWY4 ARG 71 ENGINEERED MUTATION SEQADV 1XQI ASN A 107 UNP Q8ZWY4 SER 107 ENGINEERED MUTATION SEQADV 1XQI MSE A 112 UNP Q8ZWY4 MET 112 MODIFIED RESIDUE SEQADV 1XQI ASN A 117 UNP Q8ZWY4 ILE 117 ENGINEERED MUTATION SEQADV 1XQI MSE A 120 UNP Q8ZWY4 MET 120 MODIFIED RESIDUE SEQADV 1XQI MSE B 1 UNP Q8ZWY4 MET 1 MODIFIED RESIDUE SEQADV 1XQI ASP B 10 UNP Q8ZWY4 ALA 10 ENGINEERED MUTATION SEQADV 1XQI MSE B 13 UNP Q8ZWY4 MET 13 MODIFIED RESIDUE SEQADV 1XQI ASP B 33 UNP Q8ZWY4 GLY 33 ENGINEERED MUTATION SEQADV 1XQI LYS B 40 UNP Q8ZWY4 GLU 40 ENGINEERED MUTATION SEQADV 1XQI MSE B 51 UNP Q8ZWY4 MET 51 MODIFIED RESIDUE SEQADV 1XQI GLN B 71 UNP Q8ZWY4 ARG 71 ENGINEERED MUTATION SEQADV 1XQI ASN B 107 UNP Q8ZWY4 SER 107 ENGINEERED MUTATION SEQADV 1XQI MSE B 112 UNP Q8ZWY4 MET 112 MODIFIED RESIDUE SEQADV 1XQI ASN B 117 UNP Q8ZWY4 ILE 117 ENGINEERED MUTATION SEQADV 1XQI MSE B 120 UNP Q8ZWY4 MET 120 MODIFIED RESIDUE SEQADV 1XQI MSE C 1 UNP Q8ZWY4 MET 1 MODIFIED RESIDUE SEQADV 1XQI ASP C 10 UNP Q8ZWY4 ALA 10 ENGINEERED MUTATION SEQADV 1XQI MSE C 13 UNP Q8ZWY4 MET 13 MODIFIED RESIDUE SEQADV 1XQI ASP C 33 UNP Q8ZWY4 GLY 33 ENGINEERED MUTATION SEQADV 1XQI LYS C 40 UNP Q8ZWY4 GLU 40 ENGINEERED MUTATION SEQADV 1XQI MSE C 51 UNP Q8ZWY4 MET 51 MODIFIED RESIDUE SEQADV 1XQI GLN C 71 UNP Q8ZWY4 ARG 71 ENGINEERED MUTATION SEQADV 1XQI ASN C 107 UNP Q8ZWY4 SER 107 ENGINEERED MUTATION SEQADV 1XQI MSE C 112 UNP Q8ZWY4 MET 112 MODIFIED RESIDUE SEQADV 1XQI ASN C 117 UNP Q8ZWY4 ILE 117 ENGINEERED MUTATION SEQADV 1XQI MSE C 120 UNP Q8ZWY4 MET 120 MODIFIED RESIDUE SEQRES 1 A 195 MSE HIS ALA ILE ASN ILE ALA PHE PHE ASP LEU ILE MSE SEQRES 2 A 195 PRO VAL GLU LYS THR LEU LEU ILE LEU LYS PRO ASP ALA SEQRES 3 A 195 VAL ALA ARG GLY LEU VAL ASP GLU ILE ILE SER ARG PHE SEQRES 4 A 195 LYS LYS ALA GLY LEU LYS ILE VAL ALA LEU LYS MSE VAL SEQRES 5 A 195 LYS ALA SER PRO GLU GLU ILE GLU ARG PHE TYR PRO SER SEQRES 6 A 195 SER GLU GLU TRP LEU GLN SER ALA GLY GLN LYS LEU LEU SEQRES 7 A 195 LYS ALA TYR GLN GLU LEU GLY ILE ASP PRO ARG ALA LYS SEQRES 8 A 195 ILE GLY THR ASP ASP PRO VAL GLU VAL GLY ARG ILE ILE SEQRES 9 A 195 LYS ARG ASN LEU VAL LYS TYR MSE THR SER GLY PRO ASN SEQRES 10 A 195 VAL VAL MSE VAL LEU LYS GLY ASN ARG ALA VAL GLU ILE SEQRES 11 A 195 VAL ARG LYS LEU VAL GLY PRO THR SER PRO HIS SER ALA SEQRES 12 A 195 PRO PRO GLY THR ILE ARG GLY ASP TYR SER ILE ASP SER SEQRES 13 A 195 PRO ASP LEU ALA ALA GLU GLU GLY ARG VAL VAL PHE ASN SEQRES 14 A 195 LEU VAL HIS ALA SER ASP SER PRO SER GLU ALA GLU ARG SEQRES 15 A 195 GLU ILE ARG PHE TRP PHE ARG GLU GLU GLU VAL LEU GLU SEQRES 1 B 195 MSE HIS ALA ILE ASN ILE ALA PHE PHE ASP LEU ILE MSE SEQRES 2 B 195 PRO VAL GLU LYS THR LEU LEU ILE LEU LYS PRO ASP ALA SEQRES 3 B 195 VAL ALA ARG GLY LEU VAL ASP GLU ILE ILE SER ARG PHE SEQRES 4 B 195 LYS LYS ALA GLY LEU LYS ILE VAL ALA LEU LYS MSE VAL SEQRES 5 B 195 LYS ALA SER PRO GLU GLU ILE GLU ARG PHE TYR PRO SER SEQRES 6 B 195 SER GLU GLU TRP LEU GLN SER ALA GLY GLN LYS LEU LEU SEQRES 7 B 195 LYS ALA TYR GLN GLU LEU GLY ILE ASP PRO ARG ALA LYS SEQRES 8 B 195 ILE GLY THR ASP ASP PRO VAL GLU VAL GLY ARG ILE ILE SEQRES 9 B 195 LYS ARG ASN LEU VAL LYS TYR MSE THR SER GLY PRO ASN SEQRES 10 B 195 VAL VAL MSE VAL LEU LYS GLY ASN ARG ALA VAL GLU ILE SEQRES 11 B 195 VAL ARG LYS LEU VAL GLY PRO THR SER PRO HIS SER ALA SEQRES 12 B 195 PRO PRO GLY THR ILE ARG GLY ASP TYR SER ILE ASP SER SEQRES 13 B 195 PRO ASP LEU ALA ALA GLU GLU GLY ARG VAL VAL PHE ASN SEQRES 14 B 195 LEU VAL HIS ALA SER ASP SER PRO SER GLU ALA GLU ARG SEQRES 15 B 195 GLU ILE ARG PHE TRP PHE ARG GLU GLU GLU VAL LEU GLU SEQRES 1 C 195 MSE HIS ALA ILE ASN ILE ALA PHE PHE ASP LEU ILE MSE SEQRES 2 C 195 PRO VAL GLU LYS THR LEU LEU ILE LEU LYS PRO ASP ALA SEQRES 3 C 195 VAL ALA ARG GLY LEU VAL ASP GLU ILE ILE SER ARG PHE SEQRES 4 C 195 LYS LYS ALA GLY LEU LYS ILE VAL ALA LEU LYS MSE VAL SEQRES 5 C 195 LYS ALA SER PRO GLU GLU ILE GLU ARG PHE TYR PRO SER SEQRES 6 C 195 SER GLU GLU TRP LEU GLN SER ALA GLY GLN LYS LEU LEU SEQRES 7 C 195 LYS ALA TYR GLN GLU LEU GLY ILE ASP PRO ARG ALA LYS SEQRES 8 C 195 ILE GLY THR ASP ASP PRO VAL GLU VAL GLY ARG ILE ILE SEQRES 9 C 195 LYS ARG ASN LEU VAL LYS TYR MSE THR SER GLY PRO ASN SEQRES 10 C 195 VAL VAL MSE VAL LEU LYS GLY ASN ARG ALA VAL GLU ILE SEQRES 11 C 195 VAL ARG LYS LEU VAL GLY PRO THR SER PRO HIS SER ALA SEQRES 12 C 195 PRO PRO GLY THR ILE ARG GLY ASP TYR SER ILE ASP SER SEQRES 13 C 195 PRO ASP LEU ALA ALA GLU GLU GLY ARG VAL VAL PHE ASN SEQRES 14 C 195 LEU VAL HIS ALA SER ASP SER PRO SER GLU ALA GLU ARG SEQRES 15 C 195 GLU ILE ARG PHE TRP PHE ARG GLU GLU GLU VAL LEU GLU MODRES 1XQI MSE A 51 MET SELENOMETHIONINE MODRES 1XQI MSE A 112 MET SELENOMETHIONINE MODRES 1XQI MSE A 120 MET SELENOMETHIONINE MODRES 1XQI MSE B 51 MET SELENOMETHIONINE MODRES 1XQI MSE B 112 MET SELENOMETHIONINE MODRES 1XQI MSE B 120 MET SELENOMETHIONINE MODRES 1XQI MSE C 51 MET SELENOMETHIONINE MODRES 1XQI MSE C 112 MET SELENOMETHIONINE MODRES 1XQI MSE C 120 MET SELENOMETHIONINE HET MSE A 51 8 HET MSE A 112 8 HET MSE A 120 8 HET MSE B 51 8 HET MSE B 112 8 HET MSE B 120 8 HET MSE C 51 8 HET MSE C 112 8 HET MSE C 120 8 HET TRS A 200 8 HET PGE A 500 10 HET TRS B 300 8 HET PGE B 600 10 HET TRS C 400 8 HET PGE C 700 10 HETNAM MSE SELENOMETHIONINE HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM PGE TRIETHYLENE GLYCOL HETSYN TRS TRIS BUFFER FORMUL 1 MSE 9(C5 H11 N O2 SE) FORMUL 4 TRS 3(C4 H12 N O3 1+) FORMUL 5 PGE 3(C6 H14 O4) FORMUL 10 HOH *158(H2 O) HELIX 1 1 LYS A 23 ARG A 29 1 7 HELIX 2 2 LEU A 31 GLY A 43 1 13 HELIX 3 3 SER A 55 TYR A 63 1 9 HELIX 4 4 SER A 66 GLY A 85 1 20 HELIX 5 5 ASP A 87 GLY A 93 1 7 HELIX 6 6 ASP A 96 THR A 113 1 18 HELIX 7 7 ARG A 126 GLY A 136 1 11 HELIX 8 8 SER A 139 ALA A 143 5 5 HELIX 9 9 THR A 147 SER A 153 1 7 HELIX 10 10 SER A 156 GLU A 163 1 8 HELIX 11 11 SER A 176 PHE A 188 1 13 HELIX 12 12 ARG A 189 VAL A 193 5 5 HELIX 13 13 LYS B 23 ARG B 29 1 7 HELIX 14 14 LEU B 31 ALA B 42 1 12 HELIX 15 15 SER B 55 TYR B 63 1 9 HELIX 16 16 SER B 66 GLY B 85 1 20 HELIX 17 17 ASP B 87 ILE B 92 1 6 HELIX 18 18 ASP B 96 THR B 113 1 18 HELIX 19 19 ARG B 126 GLY B 136 1 11 HELIX 20 20 SER B 139 ALA B 143 5 5 HELIX 21 21 THR B 147 SER B 153 1 7 HELIX 22 22 SER B 156 GLU B 163 1 8 HELIX 23 23 SER B 176 PHE B 188 1 13 HELIX 24 24 LYS C 23 ARG C 29 1 7 HELIX 25 25 LEU C 31 GLY C 43 1 13 HELIX 26 26 SER C 55 TYR C 63 1 9 HELIX 27 27 SER C 66 LEU C 84 1 19 HELIX 28 28 ASP C 87 ILE C 92 1 6 HELIX 29 29 ASP C 96 MSE C 112 1 17 HELIX 30 30 ARG C 126 GLY C 136 1 11 HELIX 31 31 SER C 139 ALA C 143 5 5 HELIX 32 32 THR C 147 SER C 153 1 7 HELIX 33 33 SER C 156 GLU C 163 1 8 HELIX 34 34 SER C 176 PHE C 188 1 13 HELIX 35 35 ARG C 189 VAL C 193 5 5 SHEET 1 A 4 LYS A 45 VAL A 52 0 SHEET 2 A 4 ASN A 117 LYS A 123 -1 O ASN A 117 N VAL A 52 SHEET 3 A 4 LYS A 17 LEU A 22 -1 N LEU A 22 O VAL A 118 SHEET 4 A 4 VAL A 171 ALA A 173 -1 O HIS A 172 N ILE A 21 SHEET 1 B 4 LYS B 45 VAL B 52 0 SHEET 2 B 4 ASN B 117 LYS B 123 -1 O ASN B 117 N VAL B 52 SHEET 3 B 4 LYS B 17 LEU B 22 -1 N LEU B 22 O VAL B 118 SHEET 4 B 4 VAL B 171 ALA B 173 -1 O HIS B 172 N ILE B 21 SHEET 1 C 4 LYS C 45 VAL C 52 0 SHEET 2 C 4 ASN C 117 LYS C 123 -1 O ASN C 117 N VAL C 52 SHEET 3 C 4 LYS C 17 LEU C 22 -1 N LEU C 22 O VAL C 118 SHEET 4 C 4 VAL C 171 ALA C 173 -1 O HIS C 172 N ILE C 21 LINK C LYS A 50 N MSE A 51 1555 1555 1.34 LINK C MSE A 51 N VAL A 52 1555 1555 1.33 LINK C TYR A 111 N MSE A 112 1555 1555 1.34 LINK C MSE A 112 N THR A 113 1555 1555 1.33 LINK C VAL A 119 N MSE A 120 1555 1555 1.33 LINK C MSE A 120 N VAL A 121 1555 1555 1.33 LINK C LYS B 50 N MSE B 51 1555 1555 1.33 LINK C MSE B 51 N VAL B 52 1555 1555 1.34 LINK C TYR B 111 N MSE B 112 1555 1555 1.33 LINK C MSE B 112 N THR B 113 1555 1555 1.33 LINK C VAL B 119 N MSE B 120 1555 1555 1.33 LINK C MSE B 120 N VAL B 121 1555 1555 1.33 LINK C LYS C 50 N MSE C 51 1555 1555 1.33 LINK C MSE C 51 N VAL C 52 1555 1555 1.34 LINK C TYR C 111 N MSE C 112 1555 1555 1.33 LINK C MSE C 112 N THR C 113 1555 1555 1.33 LINK C VAL C 119 N MSE C 120 1555 1555 1.32 LINK C MSE C 120 N VAL C 121 1555 1555 1.32 SITE 1 AC1 5 LYS A 23 TYR A 63 ASN A 169 HIS A 172 SITE 2 AC1 5 PGE A 500 SITE 1 AC2 8 LYS B 23 TYR B 63 THR B 138 ASN B 169 SITE 2 AC2 8 VAL B 171 HIS B 172 PGE B 600 HOH B 613 SITE 1 AC3 8 LYS C 23 TYR C 63 THR C 138 ASN C 169 SITE 2 AC3 8 HIS C 172 PGE C 700 HOH C 730 HOH C 755 SITE 1 AC4 11 TYR A 63 PRO A 64 TRP A 69 HIS A 172 SITE 2 AC4 11 ALA A 173 SER A 174 ASP A 175 GLU A 179 SITE 3 AC4 11 GLU A 183 TRS A 200 HOH A 505 SITE 1 AC5 11 TYR B 63 PRO B 64 TRP B 69 HIS B 172 SITE 2 AC5 11 ALA B 173 SER B 174 ASP B 175 GLU B 179 SITE 3 AC5 11 GLU B 183 TRS B 300 HOH B 653 SITE 1 AC6 11 TYR C 63 PRO C 64 TRP C 69 HIS C 172 SITE 2 AC6 11 ALA C 173 SER C 174 ASP C 175 GLU C 179 SITE 3 AC6 11 GLU C 183 TRS C 400 HOH C 749 CRYST1 125.022 72.041 104.993 90.00 133.30 90.00 C 1 2 1 12 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 0.007999 0.000000 0.007537 0.00000 SCALE2 0.000000 0.013881 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013087 0.00000