HEADER DE NOVO PROTEIN 20-OCT-16 5TPJ 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 5TPJ 1 REMARK REVDAT 4 04-DEC-19 5TPJ 1 REMARK REVDAT 3 20-SEP-17 5TPJ 1 REMARK REVDAT 2 01-FEB-17 5TPJ 1 JRNL REVDAT 1 25-JAN-17 5TPJ 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. 3.10 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.59 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 2881 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.340 REMARK 3 FREE R VALUE TEST SET COUNT : 269 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 45.5906 - 3.9063 1.00 1362 131 0.2071 0.2416 REMARK 3 2 3.9063 - 3.1008 1.00 1250 138 0.2537 0.3090 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.870 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 : 0.007 988 REMARK 3 ANGLE : 0.977 1340 REMARK 3 CHIRALITY : 0.038 153 REMARK 3 PLANARITY : 0.004 171 REMARK 3 DIHEDRAL : 15.982 359 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 5TPJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1000224596. 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 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 : 2927 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 56.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.7000 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: MOLECULAR REPLACEMENT 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 (%): 48.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM CITRATE DIBASIC AND 30% REMARK 280 PEG 3350, PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.55500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.90500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.90500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.27750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.90500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.90500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 84.83250 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.90500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.90500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.27750 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.90500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.90500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 84.83250 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 56.55500 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 -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 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 MET A 1 CG SD CE REMARK 470 GLU A 5 CG CD OE1 OE2 REMARK 470 LYS A 8 CG CD CE NZ REMARK 470 LYS A 18 CG CD CE NZ REMARK 470 GLN A 19 CG CD OE1 NE2 REMARK 470 GLU A 23 CG CD OE1 OE2 REMARK 470 ARG A 61 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 GLU A 94 CG CD OE1 OE2 REMARK 470 ASN A 97 CG OD1 ND2 REMARK 470 LYS A 101 CG CD CE NZ REMARK 470 GLU A 110 CG CD OE1 OE2 REMARK 470 LYS A 112 CG CD CE NZ REMARK 470 LYS A 113 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 23 -1.79 75.46 REMARK 500 PRO A 109 -48.97 -25.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TPH RELATED DB: PDB DBREF 5TPJ A -2 122 PDB 5TPJ 5TPJ -2 122 SEQRES 1 A 125 GLY SER HIS MET SER ARG GLU GLU ILE ARG LYS VAL VAL SEQRES 2 A 125 GLU GLU MET VAL ARG LYS LEU LYS GLN GLY SER PRO GLU SEQRES 3 A 125 ASP ILE SER LYS TYR LEU SER PRO ASP VAL ARG LEU GLU SEQRES 4 A 125 VAL GLY ASN TYR THR PHE GLU GLY SER GLU GLN VAL THR SEQRES 5 A 125 LYS PHE TRP ARG MET LEU THR LYS PHE VAL ASP ARG VAL SEQRES 6 A 125 GLU VAL ARG LYS VAL GLN VAL ASP GLY ASN HIS VAL ARG SEQRES 7 A 125 VAL GLU VAL GLU VAL GLU TRP ASN GLY LYS LYS TRP THR SEQRES 8 A 125 PHE GLU VAL GLU VAL GLU VAL ARG ASN GLY LYS ILE LYS SEQRES 9 A 125 ARG ILE ARG LEU GLN VAL ASP PRO GLU PHE LYS LYS VAL SEQRES 10 A 125 VAL GLN ASN ILE TRP ASN LEU LEU FORMUL 2 HOH *(H2 O) HELIX 1 AA1 SER A 2 LYS A 16 1 15 HELIX 2 AA2 GLU A 23 LYS A 27 5 5 HELIX 3 AA3 GLY A 44 LYS A 57 1 14 HELIX 4 AA4 ASP A 108 LEU A 122 1 15 SHEET 1 AA1 6 TYR A 40 GLU A 43 0 SHEET 2 AA1 6 LEU A 29 VAL A 37 -1 N LEU A 35 O PHE A 42 SHEET 3 AA1 6 LYS A 99 GLN A 106 1 O LEU A 105 N GLU A 36 SHEET 4 AA1 6 LYS A 85 ARG A 96 -1 N GLU A 92 O ARG A 104 SHEET 5 AA1 6 HIS A 73 TRP A 82 -1 N VAL A 74 O VAL A 93 SHEET 6 AA1 6 ARG A 61 ASP A 70 -1 N GLN A 68 O ARG A 75 CRYST1 49.810 49.810 113.110 90.00 90.00 90.00 P 41 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 0.020076 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020076 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008841 0.00000