HEADER DE NOVO PROTEIN 27-OCT-16 5TRV TITLE CRYSTAL STRUCTURE OF A DE NOVO DESIGNED PROTEIN WITH CURVED BETA-SHEET COMPND MOL_ID: 1; COMPND 2 MOLECULE: DENOVO NTF2; 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 BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DE NOVO NTF2, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.BASANTA,G.OBERDORFER,E.MARCOS,T.M.CHIDYAUSIKU,B.SANKARAN,D.BAKER REVDAT 5 06-MAR-24 5TRV 1 REMARK REVDAT 4 04-DEC-19 5TRV 1 REMARK REVDAT 3 20-SEP-17 5TRV 1 REMARK REVDAT 2 01-FEB-17 5TRV 1 JRNL REVDAT 1 25-JAN-17 5TRV 0 JRNL AUTH E.MARCOS,B.BASANTA,T.M.CHIDYAUSIKU,Y.TANG,G.OBERDORFER, JRNL AUTH 2 G.LIU,G.V.SWAPNA,R.GUAN,D.A.SILVA,J.DOU,J.H.PEREIRA,R.XIAO, JRNL AUTH 3 B.SANKARAN,P.H.ZWART,G.T.MONTELIONE,D.BAKER JRNL TITL PRINCIPLES FOR DESIGNING PROTEINS WITH CAVITIES FORMED BY JRNL TITL 2 CURVED BETA SHEETS. JRNL REF SCIENCE V. 355 201 2017 JRNL REFN ESSN 1095-9203 JRNL PMID 28082595 JRNL DOI 10.1126/SCIENCE.AAH7389 REMARK 2 REMARK 2 RESOLUTION. 2.91 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1616 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 3316 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.249 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.050 REMARK 3 FREE R VALUE TEST SET COUNT : 300 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 41.7371 - 3.6661 0.94 1515 159 0.2354 0.2968 REMARK 3 2 3.6661 - 2.9101 0.98 1501 141 0.2862 0.2979 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.002 928 REMARK 3 ANGLE : 0.521 1247 REMARK 3 CHIRALITY : 0.021 142 REMARK 3 PLANARITY : 0.002 163 REMARK 3 DIHEDRAL : 13.829 348 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 5TRV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1000224604. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JUN-16 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 : 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM 7.1.0 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.8 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3349 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.910 REMARK 200 RESOLUTION RANGE LOW (A) : 41.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.03400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 72.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BICINE/TRIZMA BASE, PH 8.5, 10% REMARK 280 PEG 20 000, 20% PEG MME 550 AND 0.03 M OF EACH ETHYLENE GLYCOL REMARK 280 (DIETHYLENEGLYCOL, TRIETHYLENEGLYCOL, TETRAETHYLENEGLYCOL AND REMARK 280 PENTAETHYLENEGLYCOL)., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 37.76500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.76500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.03500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.76500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.76500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 25.03500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.76500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.76500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.03500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.76500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.76500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.03500 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 LEU A 118 REMARK 465 ASN A 119 REMARK 465 TYR A 120 REMARK 465 GLY A 121 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 3 CG CD OE1 OE2 REMARK 470 ARG A 6 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 7 CG CD CE NZ REMARK 470 LYS A 14 CG CD CE NZ REMARK 470 LYS A 17 CG CD CE NZ REMARK 470 ASN A 20 CG OD1 ND2 REMARK 470 GLU A 22 CG CD OE1 OE2 REMARK 470 GLN A 23 CG CD OE1 NE2 REMARK 470 GLU A 45 CG CD OE1 OE2 REMARK 470 LYS A 49 CG CD CE NZ REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 ASP A 59 CG OD1 OD2 REMARK 470 ARG A 60 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 82 CG OD1 ND2 REMARK 470 ARG A 85 NE CZ NH1 NH2 REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 LYS A 115 CG CD CE NZ 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 GLU A 70 -119.94 55.30 REMARK 500 GLN A 116 34.30 -85.57 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 PEG A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TS4 RELATED DB: PDB DBREF 5TRV A -3 121 PDB 5TRV 5TRV -3 121 SEQRES 1 A 125 GLY SER HIS MET THR GLN GLU GLU VAL ARG LYS ILE MET SEQRES 2 A 125 GLU LYS LEU LYS LYS ALA PHE LYS GLN GLY ASN PRO GLU SEQRES 3 A 125 GLN ILE VAL SER LEU LEU SER PRO ASP VAL ARG VAL LYS SEQRES 4 A 125 VAL GLY ASN GLN GLU PHE SER GLY SER GLU GLU ALA GLU SEQRES 5 A 125 LYS MET TRP ARG LYS LEU MET LYS PHE VAL ASP ARG VAL SEQRES 6 A 125 GLU VAL ARG ARG VAL LYS VAL ASP GLU ASN ARG VAL GLU SEQRES 7 A 125 ILE GLU VAL GLU PHE GLU VAL ASN GLY GLN ARG TYR SER SEQRES 8 A 125 MET GLU PHE HIS PHE GLU VAL GLU ASN GLY LYS VAL ARG SEQRES 9 A 125 ARG VAL GLU ILE ARG ILE SER PRO THR MET LYS LYS LEU SEQRES 10 A 125 MET LYS GLN ILE LEU ASN TYR GLY HET PEG A 201 7 HETNAM PEG DI(HYDROXYETHYL)ETHER FORMUL 2 PEG C4 H10 O3 FORMUL 3 HOH *2(H2 O) HELIX 1 AA1 THR A 1 GLY A 19 1 19 HELIX 2 AA2 ASN A 20 LEU A 27 1 8 HELIX 3 AA3 GLY A 43 VAL A 58 1 16 HELIX 4 AA4 PRO A 108 LYS A 111 5 4 HELIX 5 AA5 LYS A 112 ILE A 117 5 6 SHEET 1 AA1 6 GLN A 39 SER A 42 0 SHEET 2 AA1 6 LEU A 28 VAL A 36 -1 N VAL A 34 O PHE A 41 SHEET 3 AA1 6 LYS A 98 ILE A 106 1 O VAL A 102 N LYS A 35 SHEET 4 AA1 6 ARG A 85 GLU A 95 -1 N HIS A 91 O GLU A 103 SHEET 5 AA1 6 ARG A 72 GLU A 80 -1 N VAL A 73 O PHE A 92 SHEET 6 AA1 6 VAL A 61 ASP A 69 -1 N GLU A 62 O GLU A 78 SITE 1 AC1 5 GLN A 39 PHE A 41 MET A 50 MET A 114 SITE 2 AC1 5 ILE A 117 CRYST1 75.530 75.530 50.070 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 0.013240 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013240 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019972 0.00000