HEADER DE NOVO PROTEIN 09-MAR-20 6W3W TITLE AN ENUMERATIVE ALGORITHM FOR DE NOVO DESIGN OF PROTEINS WITH DIVERSE TITLE 2 POCKET STRUCTURES 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 NTF2, DE NOVO DESIGN, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.K.BERA,B.BASANTA,F.DIMAIO,B.SANKARAN,D.BAKER REVDAT 6 03-APR-24 6W3W 1 REMARK REVDAT 5 06-MAR-24 6W3W 1 REMARK REVDAT 4 16-SEP-20 6W3W 1 JRNL REVDAT 3 09-SEP-20 6W3W 1 JRNL REVDAT 2 19-AUG-20 6W3W 1 TITLE JRNL REVDAT 1 08-APR-20 6W3W 0 JRNL AUTH B.BASANTA,M.J.BICK,A.K.BERA,C.NORN,C.M.CHOW,L.P.CARTER, JRNL AUTH 2 I.GORESHNIK,F.DIMAIO,D.BAKER JRNL TITL AN ENUMERATIVE ALGORITHM FOR DE NOVO DESIGN OF PROTEINS WITH JRNL TITL 2 DIVERSE POCKET STRUCTURES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 22135 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32839327 JRNL DOI 10.1073/PNAS.2005412117 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15RC3_3435 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15519 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1553 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 3.4500 - 2.7400 1.00 1306 146 0.1834 0.2194 REMARK 3 2 2.7400 - 2.3900 1.00 1284 142 0.1779 0.2274 REMARK 3 3 2.3900 - 2.1700 1.00 1260 139 0.1619 0.2004 REMARK 3 4 2.1700 - 2.0200 1.00 1273 142 0.1685 0.2072 REMARK 3 5 2.0200 - 1.9000 1.00 1248 139 0.2188 0.2770 REMARK 3 6 1.9000 - 1.8000 1.00 1240 138 0.2332 0.3175 REMARK 3 7 1.8000 - 1.7200 1.00 1248 139 0.2773 0.3407 REMARK 3 8 1.7200 - 1.6600 1.00 1240 137 0.3156 0.3373 REMARK 3 9 1.6600 - 1.6000 1.00 1242 139 0.3474 0.4186 REMARK 3 10 1.6000 - 1.5500 1.00 1234 137 0.3692 0.4240 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) : 0.263 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.787 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.83 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 : 0.004 923 REMARK 3 ANGLE : 0.633 1243 REMARK 3 CHIRALITY : 0.048 134 REMARK 3 PLANARITY : 0.003 163 REMARK 3 DIHEDRAL : 9.864 547 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 6W3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1000247574. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL 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) : 1.00 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15581 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 42.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 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 : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: DESIGN MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.09 M SODIUM NITRATE, 0.09 SODIUM REMARK 280 PHOSPHATE DIBASIC, 0.09 M AMMONIUM SULFATE; 0.1 M TRIS (BASE) & REMARK 280 BICINE PH 8.5; 12.5 % V/V MPD; 12.5% PEG 1000; 12.5% W/V PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 42.28800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.43200 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.43200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 21.14400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.43200 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.43200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 63.43200 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.43200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.43200 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 21.14400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.43200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.43200 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.43200 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 42.28800 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HZ1 LYS A 67 O HOH A 302 1.54 REMARK 500 O HOH A 313 O HOH A 368 2.02 REMARK 500 OE2 GLU A 16 O HOH A 301 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 313 O HOH A 353 4554 2.17 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 NO3 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 A 202 DBREF 6W3W A 1 107 PDB 6W3W 6W3W 1 107 SEQRES 1 A 107 ASP GLU ASP ARG GLU TRP ILE GLU ARG PHE ASN ARG ILE SEQRES 2 A 107 LEU ILE GLU SER LEU THR THR GLY ASP GLU HIS THR LEU SEQRES 3 A 107 LYS GLU LEU ILE ASP PRO ASN ALA ARG LEU VAL ILE ASN SEQRES 4 A 107 GLY ARG ASP ILE HIS GLY ARG GLU GLU PHE VAL ARG LEU SEQRES 5 A 107 LEU SER GLU MET GLY VAL LYS HIS PHE HIS VAL HIS ASP SEQRES 6 A 107 VAL LYS VAL VAL GLY ASN LYS ALA VAL THR ARG GLY ILE SEQRES 7 A 107 LEU TYR PHE ASN GLY ARG GLU TYR ASP VAL ASP VAL PHE SEQRES 8 A 107 THR ARG LYS ILE ASP GLY ARG TRP LEU TYR GLU SER LEU SEQRES 9 A 107 GLU VAL LYS HET NO3 A 201 4 HET NO3 A 202 4 HETNAM NO3 NITRATE ION FORMUL 2 NO3 2(N O3 1-) FORMUL 4 HOH *76(H2 O) HELIX 1 AA1 ASP A 1 GLY A 21 1 21 HELIX 2 AA2 ASP A 22 LEU A 29 1 8 HELIX 3 AA3 GLY A 45 GLY A 57 1 13 SHEET 1 AA1 6 ARG A 41 HIS A 44 0 SHEET 2 AA1 6 ILE A 30 ILE A 38 -1 N LEU A 36 O ILE A 43 SHEET 3 AA1 6 ARG A 98 VAL A 106 1 O LEU A 104 N VAL A 37 SHEET 4 AA1 6 ARG A 84 ILE A 95 -1 N PHE A 91 O SER A 103 SHEET 5 AA1 6 LYS A 72 PHE A 81 -1 N THR A 75 O VAL A 90 SHEET 6 AA1 6 HIS A 60 VAL A 69 -1 N VAL A 69 O LYS A 72 SITE 1 AC1 2 GLY A 97 HOH A 345 SITE 1 AC2 5 ARG A 51 HIS A 64 ASP A 87 HOH A 317 SITE 2 AC2 5 HOH A 335 CRYST1 48.864 48.864 84.576 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 0.020465 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020465 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011824 0.00000