HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 04-FEB-13 4J29 TITLE CRYSTAL STRUCTURE OF ENGINEERED PROTEIN. NORTHEAST STRUCTURAL GENOMICS TITLE 2 CONSORTIUM TARGET OR258. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENGINEERED PROTEIN OR258; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)GOLD; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET29B+, OR258-29.1 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, NESG, KEYWDS 2 OR258, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR S.VOROBIEV,M.SU,R.KOGA,J.SEETHARAMAN,N.KOGA,L.MAO,R.XIAO,E.KOHAN, AUTHOR 2 J.CASTELLLANOS,J.K.EVERETT,T.B.ACTON,D.BAKER,G.T.MONTELIONE,L.TONG, AUTHOR 3 J.F.HUNT,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 1 13-MAR-13 4J29 0 JRNL AUTH S.VOROBIEV,M.SU,R.KOGA,J.SEETHARAMAN,N.KOGA,L.MAO,R.XIAO, JRNL AUTH 2 E.KOHAN,J.CASTELLLANOS,J.K.EVERETT,T.B.ACTON,D.BAKER, JRNL AUTH 3 G.T.MONTELIONE,L.TONG,J.F.HUNT JRNL TITL CRYSTAL STRUCTURE OF ENGINEERED PROTEIN OR258. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.89 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 12634 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.690 REMARK 3 FREE R VALUE TEST SET COUNT : 593 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 23.8870 - 3.3310 1.00 3024 134 0.2140 0.2430 REMARK 3 2 3.3310 - 2.6450 1.00 3029 138 0.2510 0.2880 REMARK 3 3 2.6450 - 2.3110 1.00 2986 162 0.2630 0.2670 REMARK 3 4 2.3110 - 2.1000 1.00 3002 159 0.2920 0.3450 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 62.95 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.690 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.27500 REMARK 3 B22 (A**2) : 2.27500 REMARK 3 B33 (A**2) : -4.55000 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 1044 REMARK 3 ANGLE : 1.258 1401 REMARK 3 CHIRALITY : 0.094 169 REMARK 3 PLANARITY : 0.004 181 REMARK 3 DIHEDRAL : 17.096 426 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: chain A REMARK 3 ORIGIN FOR THE GROUP (A): 34.5346 25.6132 12.4845 REMARK 3 T TENSOR REMARK 3 T11: 0.2804 T22: 0.2428 REMARK 3 T33: 0.2587 T12: -0.0117 REMARK 3 T13: 0.0338 T23: 0.0045 REMARK 3 L TENSOR REMARK 3 L11: 1.1917 L22: 1.2539 REMARK 3 L33: 1.1222 L12: -0.9876 REMARK 3 L13: -0.4079 L23: -0.0062 REMARK 3 S TENSOR REMARK 3 S11: -0.2437 S12: 0.0605 S13: -0.1524 REMARK 3 S21: 0.2844 S22: 0.0726 S23: 0.1568 REMARK 3 S31: 0.1590 S32: -0.0696 S33: 0.1081 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: IN THE CRYSTAL STRUCTURE OR258 FORMS REMARK 3 DIMER WITH CRYSTAL SYMMETRY MATE (-X+1,-Y+1,Z) BY DOMAIN SWAPPING. REMARK 4 REMARK 4 4J29 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-13. REMARK 100 THE RCSB ID CODE IS RCSB077504. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97921 REMARK 200 MONOCHROMATOR : NULL 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 : 12646 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 27.600 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 28.50 REMARK 200 R MERGE FOR SHELL (I) : 1.87000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXD/E REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM NACL, 5MM DTT, 0.02% NAN3, 10MM REMARK 280 TRIS-HCL PH 7.5, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 33.77900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.77900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.45350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.77900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.77900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.45350 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.77900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.77900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.45350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.77900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.77900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 24.45350 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 67.55800 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 67.55800 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 HOH A 212 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 MSE A 1 REMARK 465 GLY A 2 REMARK 465 HIS A 130 REMARK 465 HIS A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 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 63 CG CD OE1 OE2 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 PRO A 27 3.92 -60.86 REMARK 500 THR A 62 127.07 -37.72 REMARK 500 ASP A 86 77.96 -114.79 REMARK 500 ASP A 102 -157.75 -80.44 REMARK 500 GLU A 128 103.88 -165.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 205 DISTANCE = 6.10 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NESG-OR258 RELATED DB: TARGETTRACK DBREF 4J29 A 1 134 PDB 4J29 4J29 1 134 SEQRES 1 A 134 MSE GLY THR VAL VAL ILE VAL VAL SER ARG ASP GLU ARG SEQRES 2 A 134 ILE LEU GLU GLU LEU LEU GLU VAL VAL LEU LYS SER ASP SEQRES 3 A 134 PRO ASN VAL LYS THR VAL ARG THR ASP ASP LYS GLU LYS SEQRES 4 A 134 VAL LYS GLU GLU ILE GLU LYS ALA ARG LYS GLN GLY ARG SEQRES 5 A 134 PRO ILE VAL ILE PHE ILE ARG GLY ALA THR GLU GLU VAL SEQRES 6 A 134 VAL ARG ASP ILE VAL GLU TYR ALA GLN LYS GLU GLY LEU SEQRES 7 A 134 ARG VAL LEU VAL ILE MSE VAL ASP GLN ASP GLN GLU GLU SEQRES 8 A 134 LEU GLU ARG ILE TYR GLU GLN LEU LYS LYS ASP GLY VAL SEQRES 9 A 134 ASP VAL ARG VAL THR ASP ASN GLU ASP GLU ALA LYS LYS SEQRES 10 A 134 ARG LEU LYS GLU LEU LEU GLU LYS VAL LEU GLU HIS HIS SEQRES 11 A 134 HIS HIS HIS HIS MODRES 4J29 MSE A 84 MET SELENOMETHIONINE HET MSE A 84 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *16(H2 O) HELIX 1 1 ASP A 11 ASP A 26 1 16 HELIX 2 2 ASP A 36 GLN A 50 1 15 HELIX 3 3 THR A 62 LYS A 75 1 14 HELIX 4 4 ASP A 86 ASP A 102 1 17 HELIX 5 5 ASN A 111 LEU A 127 1 17 SHEET 1 A 4 LYS A 30 ARG A 33 0 SHEET 2 A 4 ILE A 54 ILE A 58 1 O PHE A 57 N VAL A 32 SHEET 3 A 4 VAL A 4 VAL A 8 1 N VAL A 7 O ILE A 56 SHEET 4 A 4 VAL A 80 MSE A 84 1 O ILE A 83 N VAL A 8 LINK C ILE A 83 N MSE A 84 1555 1555 1.33 LINK C MSE A 84 N VAL A 85 1555 1555 1.32 CISPEP 1 GLY A 60 ALA A 61 0 -6.40 CRYST1 67.558 67.558 48.907 90.00 90.00 90.00 P 42 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 0.014802 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014802 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020447 0.00000