HEADER DE NOVO PROTEIN 12-NOV-12 4HXT TITLE CRYSTAL STRUCTURE OF ENGINEERED PROTEIN. NORTHEAST STRUCTURAL GENOMICS TITLE 2 CONSORTIUM TARGET OR329 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO PROTEIN OR329; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTIFICIAL GENE; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+ MAGIC; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET21_NESG; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: OR329-21.1 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.VOROBIEV,M.SU,F.PARMEGGIANI,J.SEETHARAMAN,P.-S.HUANG,M.MAGLAQUI, AUTHOR 2 X.XIAO,D.LEE,J.K.EVERETT,T.B.ACTON,D.BAKER,G.T.MONTELIONE,L.TONG, AUTHOR 3 J.F.HUNT,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 5 30-OCT-24 4HXT 1 REMARK REVDAT 4 06-DEC-23 4HXT 1 REMARK REVDAT 3 20-SEP-23 4HXT 1 LINK REVDAT 2 12-APR-17 4HXT 1 JRNL REVDAT 1 21-NOV-12 4HXT 0 JRNL AUTH J.A.FALLAS,G.UEDA,W.SHEFFLER,V.NGUYEN,D.E.MCNAMARA, JRNL AUTH 2 B.SANKARAN,J.H.PEREIRA,F.PARMEGGIANI,T.J.BRUNETTE,D.CASCIO, JRNL AUTH 3 T.R.YEATES,P.ZWART,D.BAKER JRNL TITL COMPUTATIONAL DESIGN OF SELF-ASSEMBLING CYCLIC PROTEIN JRNL TITL 2 HOMO-OLIGOMERS. JRNL REF NAT.CHEM. V. 9 353 2017 JRNL REFN ISSN 1755-4330 JRNL PMID 28338692 JRNL DOI 10.1038/NCHEM.2673 REMARK 2 REMARK 2 RESOLUTION. 1.95 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 28422 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 1399 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 40.1390 - 4.2010 0.99 2938 155 0.1640 0.1740 REMARK 3 2 4.2010 - 3.3350 1.00 2971 172 0.1380 0.1530 REMARK 3 3 3.3350 - 2.9130 1.00 2953 152 0.1830 0.2110 REMARK 3 4 2.9130 - 2.6470 1.00 2970 148 0.1810 0.2270 REMARK 3 5 2.6470 - 2.4570 1.00 3009 129 0.1660 0.2240 REMARK 3 6 2.4570 - 2.3120 1.00 2980 138 0.1630 0.1820 REMARK 3 7 2.3120 - 2.1970 0.99 2944 150 0.1540 0.1930 REMARK 3 8 2.1970 - 2.1010 0.85 2506 128 0.1730 0.2350 REMARK 3 9 2.1010 - 2.0200 0.72 2114 123 0.1840 0.2210 REMARK 3 10 2.0200 - 1.9500 0.54 1638 104 0.2030 0.2170 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.30 REMARK 3 SHRINKAGE RADIUS : 1.11 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 46.71 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.54100 REMARK 3 B22 (A**2) : 6.18200 REMARK 3 B33 (A**2) : -2.64100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.72900 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 : 0.005 1786 REMARK 3 ANGLE : 0.918 2423 REMARK 3 CHIRALITY : 0.074 313 REMARK 3 PLANARITY : 0.002 314 REMARK 3 DIHEDRAL : 14.148 659 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: NULL REMARK 4 REMARK 4 4HXT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-12. REMARK 100 THE DEPOSITION ID IS D_1000076054. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28434 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 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 (%) : 91.5 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.25400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 4DB8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.1M MAGNESIUM NITRATE, REMARK 280 0.1M SODIUM CITRATE, PH 4.2, MICROBATCH CRYSTALLIZATION UNDER REMARK 280 OIL, TEMPERATURE 277K 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 47.74650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.97050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.74650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.97050 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 300 REMARK: MONOMER,24.69 KD,83.5%|DIMER,49.94 KD,14.2% 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: 2070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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 94.50546 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 72.53628 REMARK 350 REMARK 350 BIOMOLECULE: 2 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 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 475 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 248 REMARK 465 HIS A 249 REMARK 465 HIS A 250 REMARK 465 HIS A 251 REMARK 465 HIS A 252 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: NESG-OR329 RELATED DB: TARGETTRACK DBREF 4HXT A 1 252 PDB 4HXT 4HXT 1 252 SEQRES 1 A 252 MSE ASN ASP VAL GLU LYS LEU VAL LYS LEU LEU THR SER SEQRES 2 A 252 THR ASP SER GLU THR GLN LYS GLU ALA ALA ARG ASP LEU SEQRES 3 A 252 ALA GLU ILE ALA SER GLY PRO ALA SER ALA ILE LYS ALA SEQRES 4 A 252 ILE VAL ASP ALA GLY GLY VAL GLU VAL LEU VAL LYS LEU SEQRES 5 A 252 LEU THR SER THR ASP SER GLU VAL GLN LYS GLU ALA ALA SEQRES 6 A 252 ARG ALA LEU ALA ASN ILE ALA SER GLY PRO ASP GLU ALA SEQRES 7 A 252 ILE LYS ALA ILE VAL ASP ALA GLY GLY VAL GLU VAL LEU SEQRES 8 A 252 VAL LYS LEU LEU THR SER THR ASP SER GLU VAL GLN LYS SEQRES 9 A 252 GLU ALA ALA ARG ALA LEU ALA ASN ILE ALA SER GLY PRO SEQRES 10 A 252 ASP GLU ALA ILE LYS ALA ILE VAL ASP ALA GLY GLY VAL SEQRES 11 A 252 GLU VAL LEU VAL LYS LEU LEU THR SER THR ASP SER GLU SEQRES 12 A 252 VAL GLN LYS GLU ALA ALA ARG ALA LEU ALA ASN ILE ALA SEQRES 13 A 252 SER GLY PRO ASP GLU ALA ILE LYS ALA ILE VAL ASP ALA SEQRES 14 A 252 GLY GLY VAL GLU VAL LEU VAL LYS LEU LEU THR SER THR SEQRES 15 A 252 ASP SER GLU VAL GLN LYS GLU ALA ALA ARG ALA LEU ALA SEQRES 16 A 252 ASN ILE ALA SER GLY PRO THR SER ALA ILE LYS ALA ILE SEQRES 17 A 252 VAL ASP ALA GLY GLY VAL GLU VAL LEU GLN LYS LEU LEU SEQRES 18 A 252 THR SER THR ASP SER GLU VAL GLN LYS GLU ALA GLN ARG SEQRES 19 A 252 ALA LEU GLU ASN ILE LYS SER GLY GLY TRP LEU GLU HIS SEQRES 20 A 252 HIS HIS HIS HIS HIS MODRES 4HXT MSE A 1 MET SELENOMETHIONINE HET MSE A 1 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *185(H2 O) HELIX 1 1 ASN A 2 LEU A 11 1 10 HELIX 2 2 ASP A 15 SER A 31 1 17 HELIX 3 3 PRO A 33 ALA A 43 1 11 HELIX 4 4 GLY A 44 LEU A 53 1 10 HELIX 5 5 ASP A 57 ALA A 72 1 16 HELIX 6 6 PRO A 75 ALA A 85 1 11 HELIX 7 7 GLY A 86 LEU A 95 1 10 HELIX 8 8 ASP A 99 ALA A 114 1 16 HELIX 9 9 PRO A 117 ALA A 127 1 11 HELIX 10 10 GLY A 128 LEU A 137 1 10 HELIX 11 11 ASP A 141 ALA A 156 1 16 HELIX 12 12 PRO A 159 ALA A 169 1 11 HELIX 13 13 GLY A 170 LEU A 179 1 10 HELIX 14 14 ASP A 183 ALA A 198 1 16 HELIX 15 15 PRO A 201 ALA A 211 1 11 HELIX 16 16 GLY A 212 LEU A 220 1 9 HELIX 17 17 LEU A 221 SER A 223 5 3 HELIX 18 18 ASP A 225 GLY A 242 1 18 LINK C MSE A 1 N ASN A 2 1555 1555 1.33 CRYST1 95.493 31.941 72.543 90.00 90.78 90.00 C 1 2 1 4 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 0.010472 0.000000 0.000142 0.00000 SCALE2 0.000000 0.031308 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013786 0.00000 HETATM 1 N MSE A 1 19.179 23.819 9.459 1.00 56.64 N ANISOU 1 N MSE A 1 6997 8029 6496 481 -219 -473 N HETATM 2 CA MSE A 1 20.614 23.636 9.835 1.00 53.62 C ANISOU 2 CA MSE A 1 6638 7571 6165 447 -212 -431 C HETATM 3 C MSE A 1 21.389 24.945 9.788 1.00 52.79 C ANISOU 3 C MSE A 1 6553 7366 6139 480 -276 -411 C HETATM 4 O MSE A 1 21.127 25.799 8.941 1.00 49.06 O ANISOU 4 O MSE A 1 6086 6863 5691 506 -313 -393 O HETATM 5 CB MSE A 1 21.309 22.671 8.874 1.00 51.51 C ANISOU 5 CB MSE A 1 6386 7288 5898 384 -154 -365 C HETATM 6 CG MSE A 1 20.842 21.239 8.909 1.00 50.43 C ANISOU 6 CG MSE A 1 6235 7227 5700 340 -91 -374 C HETATM 7 SE MSE A 1 21.966 20.215 7.742 1.00 74.29 SE ANISOU 7 SE MSE A 1 9275 10211 8741 273 -34 -300 SE HETATM 8 CE MSE A 1 20.965 20.395 6.115 1.00 91.82 C ANISOU 8 CE MSE A 1 11482 12477 10927 282 -23 -287 C