HEADER UNKNOWN FUNCTION 06-MAY-04 1VK9 TITLE CRYSTAL STRUCTURE OF A DUF1893 FAMILY PROTEIN (TM1506) FROM THERMOTOGA TITLE 2 MARITIMA AT 2.70 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONSERVED HYPOTHETICAL PROTEIN TM1506; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: TM1506; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 10 20-NOV-24 1VK9 1 REMARK REVDAT 9 25-JAN-23 1VK9 1 REMARK SEQADV LINK REVDAT 8 04-OCT-17 1VK9 1 REMARK REVDAT 7 13-JUL-11 1VK9 1 VERSN REVDAT 6 28-JUL-10 1VK9 1 HEADER TITLE KEYWDS REVDAT 5 24-FEB-09 1VK9 1 VERSN REVDAT 4 23-SEP-08 1VK9 1 JRNL REVDAT 3 28-MAR-06 1VK9 1 JRNL REVDAT 2 18-JAN-05 1VK9 1 AUTHOR KEYWDS REMARK REVDAT 1 18-MAY-04 1VK9 0 JRNL AUTH Q.XU,P.KOZBIAL,D.MCMULLAN,S.S.KRISHNA,S.M.BRITTAIN, JRNL AUTH 2 S.B.FICARRO,M.DIDONATO,M.D.MILLER,P.ABDUBEK,H.L.AXELROD, JRNL AUTH 3 H.J.CHIU,T.CLAYTON,L.DUAN,M.A.ELSLIGER,J.FEUERHELM, JRNL AUTH 4 S.K.GRZECHNIK,J.HALE,G.W.HAN,L.JAROSZEWSKI,H.E.KLOCK, JRNL AUTH 5 A.T.MORSE,E.NIGOGHOSSIAN,J.PAULSEN,R.REYES,C.L.RIFE, JRNL AUTH 6 H.VAN DEN BEDEM,A.WHITE,K.O.HODGSON,J.WOOLEY,A.M.DEACON, JRNL AUTH 7 A.GODZIK,S.A.LESLEY,I.A.WILSON JRNL TITL CRYSTAL STRUCTURE OF AN ADP-RIBOSYLATED PROTEIN WITH A JRNL TITL 2 CYTIDINE DEAMINASE-LIKE FOLD, BUT UNKNOWN FUNCTION (TM1506), JRNL TITL 3 FROM THERMOTOGA MARITIMA AT 2.70 A RESOLUTION. JRNL REF PROTEINS V. 71 1546 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18275082 JRNL DOI 10.1002/PROT.21992 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 9155 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 465 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 12 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.82 REMARK 3 REFLECTION IN BIN (WORKING SET) : 887 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3340 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.4560 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1151 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 9 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 75.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.42000 REMARK 3 B22 (A**2) : 0.42000 REMARK 3 B33 (A**2) : -0.64000 REMARK 3 B12 (A**2) : 0.21000 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): 0.300 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.252 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.168 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.772 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1176 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1577 ; 1.504 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 146 ; 5.523 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 176 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 846 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 544 ; 0.312 ; 0.200 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): 29 ; 0.218 ; 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): 39 ; 0.247 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.143 ; 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): 732 ; 1.758 ; 3.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1177 ; 3.422 ; 5.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 444 ; 7.109 ; 8.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 400 ;10.817 ;11.000 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -10 A 136 REMARK 3 ORIGIN FOR THE GROUP (A): 17.9770 62.1040 37.9580 REMARK 3 T TENSOR REMARK 3 T11: 0.1866 T22: 0.5788 REMARK 3 T33: 0.2187 T12: -0.0728 REMARK 3 T13: 0.0225 T23: 0.0166 REMARK 3 L TENSOR REMARK 3 L11: 5.8079 L22: 2.3452 REMARK 3 L33: 1.8169 L12: -1.4426 REMARK 3 L13: -0.9293 L23: 0.1555 REMARK 3 S TENSOR REMARK 3 S11: 0.0888 S12: -1.2350 S13: -0.0878 REMARK 3 S21: 0.1623 S22: 0.1379 S23: 0.2366 REMARK 3 S31: -0.0898 S32: 0.0375 S33: -0.2266 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 201 A 201 REMARK 3 ORIGIN FOR THE GROUP (A): 7.2440 67.3930 41.7830 REMARK 3 T TENSOR REMARK 3 T11: 0.1025 T22: 0.1546 REMARK 3 T33: 0.0629 T12: 0.0730 REMARK 3 T13: 0.0781 T23: 0.0369 REMARK 3 L TENSOR REMARK 3 L11: 8.8792 L22: 5.7071 REMARK 3 L33: 0.3174 L12: 9.6866 REMARK 3 L13: 11.9416 L23: 6.1962 REMARK 3 S TENSOR REMARK 3 S11: -0.3049 S12: -0.6762 S13: 0.0862 REMARK 3 S21: 0.5837 S22: -0.0779 S23: 0.0819 REMARK 3 S31: -0.6669 S32: -0.1624 S33: 0.3828 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THERE ARE UNEXPLAINED ELECTRON DENSITY REMARK 3 NEAR HIS -5, HIS 0, SER 31, GLU 126, GLU 127. AN UNKNOWN ENTITY REMARK 3 WAS PRESENT IN THE ACTIVE SITE, IT MAY CONTAIN FRAGMENTS SUCH AS REMARK 3 A SUGAR, A METAL AND A PHOSPHORYL GROUP, ACCORDING TO DENSITY REMARK 3 MAP. THE METALS WERE MODELLED AS ZINC SINCE THE CRYSTAL WAS REMARK 3 GROWN IN 0.2M ZINC BUFFER. LYS -7 FROM AN ADJACENT MOLECULE IN REMARK 3 THE CRYSTAL IS OBSERVED TO PARTICIPATE IN THE COORDINATION OF ZN REMARK 3 5 IN THE DENSITY MAP. IT IS SUSPICIOUS AND COULD BE AN ARTIFACT REMARK 3 OF THE LIMITED RESOLUTION. REMARK 4 REMARK 4 1VK9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-04. REMARK 100 THE DEPOSITION ID IS D_1000001943. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796, 1.0332, 0.9795 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 4.2), CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9700 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 66.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.54800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXD, AUTOSHARP, SOLOMON REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.49 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% PEG-600, 0.1M IMIDAZOLE PH 8.0, REMARK 280 0.2M ZN(OAC)2, PH 5.8, VAPOR DIFFUSION,SITTING DROP,NANODROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.25267 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.12633 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 44.25267 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.12633 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 44.25267 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 22.12633 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 44.25267 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 22.12633 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: MONOMERIC 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 14720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -950.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 66.44550 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 115.08698 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 44.25267 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 66.44550 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 115.08698 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 44.25267 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 ZN ZN A 145 LIES ON A SPECIAL POSITION. 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 -11 REMARK 465 THR A 137 REMARK 465 SER A 138 REMARK 465 LEU A 139 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 GLU A 2 CD OE1 OE2 REMARK 470 LYS A 3 CD CE NZ REMARK 470 ARG A 7 CZ NH1 NH2 REMARK 470 LYS A 37 CD CE NZ REMARK 470 LYS A 107 CG CD CE NZ REMARK 470 LYS A 110 CG CD CE NZ REMARK 470 GLU A 126 CD OE1 OE2 REMARK 470 GLU A 127 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 OE2 GLU A 99 O28 UNL A 201 1.80 REMARK 500 OD1 ASP A 56 O4 UNL A 201 1.95 REMARK 500 O28 UNL A 201 O HOH A 210 1.99 REMARK 500 SG CYS A 113 O29 UNL A 201 2.00 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 98 CB - CG - OD2 ANGL. DEV. = 6.1 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 17 58.04 35.07 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 ZN A 141 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A -8 OD1 REMARK 620 2 ASP A -8 OD2 51.5 REMARK 620 3 HIS A -3 ND1 84.3 108.5 REMARK 620 4 HIS A -1 NE2 87.0 110.7 120.8 REMARK 620 5 HOH A 204 O 167.8 116.5 99.5 100.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 144 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A -7 NZ REMARK 620 2 ASP A 124 OD1 98.4 REMARK 620 3 HOH A 202 O 104.6 126.3 REMARK 620 4 HOH A 207 O 113.1 102.4 111.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 145 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A -5 ND1 REMARK 620 2 HIS A -5 ND1 112.7 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 142 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A -4 ND1 REMARK 620 2 HIS A -2 NE2 120.8 REMARK 620 3 ASP A 47 OD1 102.0 85.7 REMARK 620 4 ASP A 47 OD2 114.7 116.6 54.2 REMARK 620 5 GLU A 50 OE1 104.7 106.7 138.3 85.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 143 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 76 NE2 REMARK 620 2 ASP A 98 OD2 105.5 REMARK 620 3 HOH A 203 O 108.6 91.3 REMARK 620 4 HOH A 205 O 107.3 119.0 123.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 140 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 90 OE1 REMARK 620 2 GLU A 90 OE2 55.1 REMARK 620 3 GLU A 90 OE1 141.2 88.9 REMARK 620 4 GLU A 90 OE2 94.5 80.3 62.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 140 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 141 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 142 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 143 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 144 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 145 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UNL A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 283363 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 FOR THE VAL/MET CONFLICT AT RESIDUE 1: REMARK 999 THIS GENE USES AN ALTERNATE INITIATION CODON REMARK 999 THAT RESULTS IN A VALINE AT POSITION 1 WHEN REMARK 999 EXPRESSED AS A FUSION. DBREF 1VK9 A 1 139 UNP Q9X1J4 Q9X1J4_THEMA 1 139 SEQADV 1VK9 MET A -11 UNP Q9X1J4 EXPRESSION TAG SEQADV 1VK9 GLY A -10 UNP Q9X1J4 EXPRESSION TAG SEQADV 1VK9 SER A -9 UNP Q9X1J4 EXPRESSION TAG SEQADV 1VK9 ASP A -8 UNP Q9X1J4 EXPRESSION TAG SEQADV 1VK9 LYS A -7 UNP Q9X1J4 EXPRESSION TAG SEQADV 1VK9 ILE A -6 UNP Q9X1J4 EXPRESSION TAG SEQADV 1VK9 HIS A -5 UNP Q9X1J4 EXPRESSION TAG SEQADV 1VK9 HIS A -4 UNP Q9X1J4 EXPRESSION TAG SEQADV 1VK9 HIS A -3 UNP Q9X1J4 EXPRESSION TAG SEQADV 1VK9 HIS A -2 UNP Q9X1J4 EXPRESSION TAG SEQADV 1VK9 HIS A -1 UNP Q9X1J4 EXPRESSION TAG SEQADV 1VK9 HIS A 0 UNP Q9X1J4 EXPRESSION TAG SEQADV 1VK9 VAL A 1 UNP Q9X1J4 MET 1 SEE REMARK 999 SEQADV 1VK9 MSE A 58 UNP Q9X1J4 MET 58 MODIFIED RESIDUE SEQADV 1VK9 MSE A 70 UNP Q9X1J4 MET 70 MODIFIED RESIDUE SEQADV 1VK9 MSE A 88 UNP Q9X1J4 MET 88 MODIFIED RESIDUE SEQADV 1VK9 MSE A 112 UNP Q9X1J4 MET 112 MODIFIED RESIDUE SEQADV 1VK9 MSE A 122 UNP Q9X1J4 MET 122 MODIFIED RESIDUE SEQRES 1 A 151 MET GLY SER ASP LYS ILE HIS HIS HIS HIS HIS HIS VAL SEQRES 2 A 151 GLU LYS ASN LEU LEU ARG SER ALA LEU LYS ILE PHE GLU SEQRES 3 A 151 LYS LYS ASP LEU SER LEU LEU ALA TYR SER GLY ARG SER SEQRES 4 A 151 ILE PHE GLU SER LYS ASP SER GLY LEU LYS PRO VAL VAL SEQRES 5 A 151 GLU LEU PHE LYS ARG PHE ASP ASN LEU GLU GLY SER LEU SEQRES 6 A 151 VAL ILE ASP LYS MSE VAL GLY LYS ALA ALA ALA SER PHE SEQRES 7 A 151 LEU LEU LYS MSE LYS PRO ASP HIS ILE HIS ALA LYS VAL SEQRES 8 A 151 ILE SER LYS PRO ALA LEU LYS LEU MSE ASN GLU TYR GLY SEQRES 9 A 151 GLN SER PHE SER TYR ASP GLU LYS ILE PRO PHE VAL LEU SEQRES 10 A 151 GLY LYS ASP GLY LYS SER MSE CYS PRO PHE GLU LYS LEU SEQRES 11 A 151 VAL LEU GLU MSE ASP ASP PRO GLU GLU ILE ILE ARG ILE SEQRES 12 A 151 VAL LEU SER LYS PHE THR SER LEU MODRES 1VK9 MSE A 58 MET SELENOMETHIONINE MODRES 1VK9 MSE A 70 MET SELENOMETHIONINE MODRES 1VK9 MSE A 88 MET SELENOMETHIONINE MODRES 1VK9 MSE A 112 MET SELENOMETHIONINE MODRES 1VK9 MSE A 122 MET SELENOMETHIONINE HET MSE A 58 8 HET MSE A 70 8 HET MSE A 88 8 HET MSE A 112 8 HET MSE A 122 8 HET ZN A 140 1 HET ZN A 141 1 HET ZN A 142 1 HET ZN A 143 1 HET ZN A 144 1 HET ZN A 145 1 HET UNL A 201 29 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM UNL UNKNOWN LIGAND FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 ZN 6(ZN 2+) FORMUL 9 HOH *9(H2 O) HELIX 1 1 GLU A 2 LYS A 16 1 15 HELIX 2 2 LEU A 36 PHE A 46 1 11 HELIX 3 3 GLY A 60 LYS A 71 1 12 HELIX 4 4 LYS A 82 TYR A 91 1 10 HELIX 5 5 CYS A 113 GLU A 121 1 9 HELIX 6 6 ASP A 124 SER A 134 1 11 SHEET 1 A 5 SER A 27 SER A 31 0 SHEET 2 A 5 LEU A 20 TYR A 23 -1 N ALA A 22 O ILE A 28 SHEET 3 A 5 LEU A 53 VAL A 59 -1 O LEU A 53 N TYR A 23 SHEET 4 A 5 HIS A 74 SER A 81 1 O VAL A 79 N VAL A 59 SHEET 5 A 5 PHE A 95 ILE A 101 1 O SER A 96 N ALA A 77 LINK C LYS A 57 N MSE A 58 1555 1555 1.33 LINK C MSE A 58 N VAL A 59 1555 1555 1.33 LINK C LYS A 69 N MSE A 70 1555 1555 1.33 LINK C MSE A 70 N LYS A 71 1555 1555 1.33 LINK C LEU A 87 N MSE A 88 1555 1555 1.33 LINK C MSE A 88 N ASN A 89 1555 1555 1.34 LINK C SER A 111 N MSE A 112 1555 1555 1.34 LINK C MSE A 112 N CYS A 113 1555 1555 1.34 LINK C GLU A 121 N MSE A 122 1555 1555 1.33 LINK C MSE A 122 N ASP A 123 1555 1555 1.34 LINK OD1 ASP A -8 ZN ZN A 141 1555 1555 2.70 LINK OD2 ASP A -8 ZN ZN A 141 1555 1555 2.02 LINK NZ LYS A -7 ZN ZN A 144 7555 1555 2.05 LINK ND1 HIS A -5 ZN ZN A 145 1555 1555 2.41 LINK ND1 HIS A -5 ZN ZN A 145 4665 1555 2.42 LINK ND1 HIS A -4 ZN ZN A 142 1555 1555 1.99 LINK ND1 HIS A -3 ZN ZN A 141 4665 1555 2.03 LINK NE2 HIS A -2 ZN ZN A 142 1555 1555 2.05 LINK NE2 HIS A -1 ZN ZN A 141 4665 1555 1.97 LINK OD1 ASP A 47 ZN ZN A 142 4665 1555 2.51 LINK OD2 ASP A 47 ZN ZN A 142 4665 1555 2.11 LINK OE1 GLU A 50 ZN ZN A 142 1555 1555 1.78 LINK NE2 HIS A 76 ZN ZN A 143 1555 1555 2.06 LINK OE1 GLU A 90 ZN ZN A 140 1555 1555 2.18 LINK OE2 GLU A 90 ZN ZN A 140 1555 1555 2.46 LINK OE1 GLU A 90 ZN ZN A 140 10665 1555 2.05 LINK OE2 GLU A 90 ZN ZN A 140 10665 1555 2.13 LINK OD2 ASP A 98 ZN ZN A 143 1555 1555 1.85 LINK OD1 ASP A 124 ZN ZN A 144 1555 1555 1.88 LINK ZN ZN A 141 O HOH A 204 1555 4665 2.54 LINK ZN ZN A 143 O HOH A 203 1555 1555 2.21 LINK ZN ZN A 143 O HOH A 205 1555 1555 2.73 LINK ZN ZN A 144 O HOH A 202 1555 7555 2.35 LINK ZN ZN A 144 O HOH A 207 1555 1555 2.55 SITE 1 AC1 2 GLU A 90 ASP A 123 SITE 1 AC2 4 ASP A -8 HIS A -3 HIS A -1 HOH A 204 SITE 1 AC3 4 HIS A -2 HIS A -4 ASP A 47 GLU A 50 SITE 1 AC4 4 HIS A 76 ASP A 98 HOH A 203 HOH A 205 SITE 1 AC5 4 LYS A -7 ASP A 124 HOH A 202 HOH A 207 SITE 1 AC6 1 HIS A -5 SITE 1 AC7 17 SER A 19 SER A 34 GLY A 35 PRO A 38 SITE 2 AC7 17 ASP A 56 LYS A 57 MSE A 58 GLY A 60 SITE 3 AC7 17 LYS A 61 ALA A 62 ALA A 63 GLU A 99 SITE 4 AC7 17 CYS A 113 PHE A 115 GLU A 116 HOH A 208 SITE 5 AC7 17 HOH A 210 CRYST1 132.891 132.891 66.379 90.00 90.00 120.00 P 62 2 2 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 0.007525 0.004345 0.000000 0.00000 SCALE2 0.000000 0.008689 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015065 0.00000