HEADER BIOSYNTHETIC PROTEIN 09-MAR-20 6W3D TITLE RD1NTF2_05 WITH LONG SHEET COMPND MOL_ID: 1; COMPND 2 MOLECULE: RD1NTF2_05; 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; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: LEMO21; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET29B KEYWDS NTF2-LIKE, SYNTHETIC, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.J.BICK,B.BASANTA,B.SANKARAN,D.BAKER REVDAT 6 03-APR-24 6W3D 1 REMARK REVDAT 5 06-MAR-24 6W3D 1 REMARK REVDAT 4 23-JUN-21 6W3D 1 AUTHOR REVDAT 3 16-SEP-20 6W3D 1 JRNL REVDAT 2 09-SEP-20 6W3D 1 JRNL REVDAT 1 15-APR-20 6W3D 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. 1.38 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV-3026 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) : 1.38 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 22779 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.770 REMARK 3 FREE R VALUE TEST SET COUNT : 1997 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 28.2750 - 3.3243 0.98 1530 148 0.1926 0.2119 REMARK 3 2 3.3243 - 2.6392 1.00 1500 143 0.1933 0.1956 REMARK 3 3 2.6392 - 2.3058 1.00 1505 145 0.1664 0.1917 REMARK 3 4 2.3058 - 2.0951 1.00 1474 142 0.1521 0.2059 REMARK 3 5 2.0951 - 1.9449 1.00 1487 144 0.1478 0.2117 REMARK 3 6 1.9449 - 1.8303 1.00 1487 143 0.1526 0.2277 REMARK 3 7 1.8303 - 1.7386 1.00 1487 143 0.1696 0.2233 REMARK 3 8 1.7386 - 1.6630 1.00 1464 140 0.1770 0.2380 REMARK 3 9 1.6630 - 1.5989 1.00 1471 142 0.1807 0.2187 REMARK 3 10 1.5989 - 1.5438 1.00 1499 144 0.1829 0.3022 REMARK 3 11 1.5438 - 1.4955 1.00 1455 139 0.2078 0.2248 REMARK 3 12 1.4955 - 1.4528 1.00 1467 142 0.2405 0.3087 REMARK 3 13 1.4528 - 1.4145 1.00 1492 143 0.2716 0.3289 REMARK 3 14 1.4145 - 1.3800 1.00 1464 139 0.3205 0.3533 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.800 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.20 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 : 0.019 963 REMARK 3 ANGLE : 1.549 1305 REMARK 3 CHIRALITY : 0.115 157 REMARK 3 PLANARITY : 0.010 172 REMARK 3 DIHEDRAL : 19.415 349 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 6W3D 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_1000247548. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-18 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 : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999995 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 JUN 17, 2015 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22794 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.380 REMARK 200 RESOLUTION RANGE LOW (A) : 28.275 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.38 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 1.90900 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 REMARK 200 STARTING MODEL: COMPUTATIONAL DESIGN MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN AT 56MG/ML, THEN 1:1 DILUTION REMARK 280 IN 0.09M SODIUM FLUORIDE; 0.09M SODIUM BROMIDE; 0.09M SODIUM REMARK 280 IODIDE, 0.1M TRIS/BICINE PH 8.5, 50% V/V OF 40% V/V PEG 500 MME; REMARK 280 20 % W/V PEG 20000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K 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 30.03800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.24900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.03800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.24900 REMARK 290 SMTRY3 4 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 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 MET A -21 REMARK 465 GLY A -20 REMARK 465 SER A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 GLY A -12 REMARK 465 SER A -11 REMARK 465 GLU A -10 REMARK 465 ASN A -9 REMARK 465 SER A -4 REMARK 465 GLY A -3 REMARK 465 SER A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 ASP A 1 REMARK 465 GLU A 2 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 LEU A -8 CG CD1 CD2 REMARK 470 TYR A -7 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 PHE A -6 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN A -5 CG CD OE1 NE2 REMARK 470 ASN A 3 N CA CB CG OD1 ND2 REMARK 470 ASP A 4 CG OD1 OD2 REMARK 470 ARG A 7 CD NE CZ NH1 NH2 REMARK 470 LYS A 8 CG CD CE NZ REMARK 470 LYS A 11 CD CE NZ REMARK 470 ASP A 39 CG OD1 OD2 REMARK 470 LYS A 40 CD CE NZ REMARK 470 GLU A 46 CD OE1 OE2 REMARK 470 LYS A 50 NZ REMARK 470 LYS A 57 CG CD CE NZ REMARK 470 ARG A 58 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 72 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 73 CG OD1 ND2 REMARK 470 ARG A 83 CZ NH1 NH2 REMARK 470 HIS A 86 CG ND1 CD2 CE1 NE2 REMARK 470 ASN A 87 CG OD1 ND2 REMARK 470 ARG A 92 CD NE CZ NH1 NH2 REMARK 470 ASP A 101 CG OD1 OD2 REMARK 470 LYS A 105 CD CE NZ REMARK 470 LYS A 112 CE NZ REMARK 470 GLY A 114 C O 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 H GLY A 88 O HOH A 201 1.12 REMARK 500 HE21 GLN A 28 O HOH A 202 1.58 REMARK 500 N GLY A 88 O HOH A 201 1.84 REMARK 500 NE2 GLN A 28 O HOH A 202 2.08 REMARK 500 REMARK 500 REMARK: NULL DBREF 6W3D A -21 114 PDB 6W3D 6W3D -21 114 SEQRES 1 A 136 MET GLY SER HIS HIS HIS HIS HIS HIS GLY SER GLU ASN SEQRES 2 A 136 LEU TYR PHE GLN SER GLY SER GLY SER ASP GLU ASN ASP SEQRES 3 A 136 THR ALA ARG LYS ILE ILE LYS THR LEU LEU ASP ILE MET SEQRES 4 A 136 ARG GLU GLY ASP GLU ASP LYS LEU ARG ASP GLN MET ASP SEQRES 5 A 136 PRO ASN VAL ARG ALA ASP VAL GLY ASP LYS THR VAL HIS SEQRES 6 A 136 GLY ARG GLU HIS ALA ALA LYS PHE LEU ALA HIS ILE VAL SEQRES 7 A 136 LYS ARG ALA ASP HIS ILE SER ILE THR LEU LYS SER LEU SEQRES 8 A 136 HIS ASN HIS ASN GLY ARG LEU ARG MET GLN ALA GLU VAL SEQRES 9 A 136 ARG ILE VAL HIS ASN GLY ARG THR GLU ARG VAL THR LEU SEQRES 10 A 136 GLU MET VAL PHE ARG ASP HIS ASN GLY LYS LEU LEU ILE SEQRES 11 A 136 GLU ARG MET LYS TYR GLY FORMUL 2 HOH *57(H2 O) HELIX 1 AA1 ASP A 4 GLY A 20 1 17 HELIX 2 AA2 ASP A 21 ASP A 27 1 7 HELIX 3 AA3 GLY A 44 ARG A 58 1 15 SHEET 1 AA1 6 LYS A 40 HIS A 43 0 SHEET 2 AA1 6 MET A 29 VAL A 37 -1 N ALA A 35 O VAL A 42 SHEET 3 AA1 6 LYS A 105 TYR A 113 1 O MET A 111 N ASP A 36 SHEET 4 AA1 6 ARG A 89 ARG A 100 -1 N GLU A 96 O ARG A 110 SHEET 5 AA1 6 ARG A 75 HIS A 86 -1 N VAL A 82 O VAL A 93 SHEET 6 AA1 6 HIS A 61 HIS A 72 -1 N THR A 65 O GLU A 81 CRYST1 60.076 30.498 61.099 90.00 97.84 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 0.016646 0.000000 0.002291 0.00000 SCALE2 0.000000 0.032789 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016521 0.00000