HEADER DE NOVO PROTEIN 21-MAR-14 4PWW TITLE CRYSTAL STRUCTURE OF ENGINEERED PROTEIN. NORTHEAST STRUCTURAL GENOMICS TITLE 2 CONSORTIUM TARGET OR494. COMPND MOL_ID: 1; COMPND 2 MOLECULE: OR494; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_COMMON: ARTIFICIAL GENE; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET21_NESG; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: OR494-21.1 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, DE NOVO, OR494, DE KEYWDS 3 NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.VOROBIEV,Y.-R.LIN,J.SEETHARAMAN,R.XIAO,J.K.EVERETT,T.B.ACTON, AUTHOR 2 D.BAKER,G.T.MONTELIONE,L.TONG,J.F.HUNT,NORTHEAST STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (NESG) REVDAT 3 20-SEP-23 4PWW 1 REMARK REVDAT 2 25-OCT-17 4PWW 1 REMARK REVDAT 1 09-APR-14 4PWW 0 JRNL AUTH S.VOROBIEV,Y.-R.LIN,J.SEETHARAMAN,R.XIAO,J.K.EVERETT, JRNL AUTH 2 T.B.ACTON,D.BAKER,G.T.MONTELIONE,L.TONG,J.F.HUNT JRNL TITL CRYSTAL STRUCTURE OF ENGINEERED PROTEIN OR494. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.47 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.2_869 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.47 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 27452 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1390 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 36.5800 - 3.1680 1.00 2703 125 0.1890 0.2110 REMARK 3 2 3.1680 - 2.5140 0.99 2668 129 0.1810 0.2120 REMARK 3 3 2.5140 - 2.1970 0.99 2633 142 0.1530 0.1890 REMARK 3 4 2.1970 - 1.9960 0.99 2635 153 0.1600 0.1880 REMARK 3 5 1.9960 - 1.8530 0.98 2653 112 0.1660 0.2130 REMARK 3 6 1.8530 - 1.7430 0.97 2609 140 0.1690 0.2470 REMARK 3 7 1.7430 - 1.6560 0.97 2559 139 0.1730 0.2560 REMARK 3 8 1.6560 - 1.5840 0.97 2579 175 0.1880 0.2830 REMARK 3 9 1.5840 - 1.5230 0.96 2565 139 0.1950 0.2180 REMARK 3 10 1.5230 - 1.4710 0.92 2458 136 0.2720 0.3250 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 50.12 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.040 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.38 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.68500 REMARK 3 B22 (A**2) : 9.32400 REMARK 3 B33 (A**2) : -5.63900 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 : 0.006 694 REMARK 3 ANGLE : 0.936 927 REMARK 3 CHIRALITY : 0.057 106 REMARK 3 PLANARITY : 0.003 119 REMARK 3 DIHEDRAL : 11.540 263 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 PRESENCE OF PHOSPHATE AND ACETATE IONS WERE TRACED BACK TO A REMARK 3 PURIFICATION PROCEDURE. REMARK 3 THERE IS UNKNOWN LIGAND IN THE STRUCTURE WHICH WAS MODELED BY REMARK 3 WATER MOLECULES (A593-596). REMARK 4 REMARK 4 4PWW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000085320. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97907 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27476 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 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 (%) : 97.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.2500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.40300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 4KY3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 100MM NACL, 5MM DTT, REMARK 280 0.02% NAN3, 10MM TRIS-HCL (PH 7.5). RESERVOIR SOLUTION: 2.0M REMARK 280 AMMONIUM SULFATE, 0.1M CITRIC ACID, PH 3.5, MICROBATCH REMARK 280 CRYSTALLIZATION UNDER OIL, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 16.77400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.56900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.82250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.56900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.77400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.82250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 16.77400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.82250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 36.56900 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.82250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 16.77400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 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 36.56900 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 300 REMARK: DIMER AS REPORTED BY HPLC+LIGHT SCATTERING 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: 2360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 69.64500 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 109.70700 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 502 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 571 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 593 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 HIS A 86 REMARK 465 HIS A 87 REMARK 465 HIS A 88 REMARK 465 HIS A 89 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NESG-OR494 RELATED DB: TARGETTRACK DBREF 4PWW A 1 89 PDB 4PWW 4PWW 1 89 SEQRES 1 A 89 MET GLU MET ASP ILE ARG PHE ARG GLY ASP ASP LEU GLU SEQRES 2 A 89 ALA LEU LEU LYS ALA ALA ILE GLU MET ILE LYS GLN ALA SEQRES 3 A 89 LEU LYS PHE GLY ALA THR ILE THR LEU SER LEU ASP GLY SEQRES 4 A 89 ASN ASP LEU GLU ILE ARG ILE THR GLY VAL PRO GLU GLN SEQRES 5 A 89 VAL ARG LYS GLU LEU ALA LYS GLU ALA GLU ARG LEU ALA SEQRES 6 A 89 LYS GLU PHE GLY ILE THR VAL THR ARG THR ILE ARG GLY SEQRES 7 A 89 SER TRP SER LEU GLU HIS HIS HIS HIS HIS HIS HET PO4 A 301 5 HET ACY A 302 4 HET ACY A 303 4 HET ACY A 304 4 HETNAM PO4 PHOSPHATE ION HETNAM ACY ACETIC ACID FORMUL 2 PO4 O4 P 3- FORMUL 3 ACY 3(C2 H4 O2) FORMUL 6 HOH *96(H2 O) HELIX 1 1 ASP A 11 PHE A 29 1 19 HELIX 2 2 PRO A 50 GLY A 69 1 20 HELIX 3 3 SER A 79 GLU A 83 5 5 SHEET 1 A 4 THR A 32 ASP A 38 0 SHEET 2 A 4 ASP A 41 THR A 47 -1 O ARG A 45 N THR A 34 SHEET 3 A 4 MET A 3 ARG A 8 -1 N ILE A 5 O ILE A 44 SHEET 4 A 4 THR A 71 ARG A 74 -1 O THR A 71 N ARG A 8 SITE 1 AC1 8 ARG A 54 ARG A 74 ARG A 77 HOH A 503 SITE 2 AC1 8 HOH A 537 HOH A 552 HOH A 554 HOH A 558 SITE 1 AC2 3 PRO A 50 GLU A 51 ARG A 54 SITE 1 AC3 5 ARG A 8 GLU A 43 SER A 81 HOH A 508 SITE 2 AC3 5 HOH A 592 SITE 1 AC4 6 GLU A 62 LYS A 66 ARG A 77 TRP A 80 SITE 2 AC4 6 HOH A 565 HOH A 587 CRYST1 33.548 69.645 73.138 90.00 90.00 90.00 I 21 21 21 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 0.029808 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014359 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013673 0.00000