HEADER DE NOVO PROTEIN 09-APR-18 6CZJ TITLE STRUCTURE OF A REDESIGNED BETA BARREL, B10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: B10; COMPND 3 CHAIN: A, B; 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 KEYWDS BETA BARREL, ROSSETTA, COMPUTATIONAL, DE NOVO, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.A.DOYLE,B.L.STODDARD REVDAT 6 13-MAR-24 6CZJ 1 REMARK REVDAT 5 01-JAN-20 6CZJ 1 REMARK REVDAT 4 17-APR-19 6CZJ 1 COMPND REVDAT 3 10-OCT-18 6CZJ 1 COMPND JRNL REVDAT 2 26-SEP-18 6CZJ 1 JRNL REVDAT 1 19-SEP-18 6CZJ 0 JRNL AUTH J.DOU,A.A.VOROBIEVA,W.SHEFFLER,L.A.DOYLE,H.PARK,M.J.BICK, JRNL AUTH 2 B.MAO,G.W.FOIGHT,M.Y.LEE,L.A.GAGNON,L.CARTER,B.SANKARAN, JRNL AUTH 3 S.OVCHINNIKOV,E.MARCOS,P.S.HUANG,J.C.VAUGHAN,B.L.STODDARD, JRNL AUTH 4 D.BAKER JRNL TITL DE NOVO DESIGN OF A FLUORESCENCE-ACTIVATING BETA-BARREL. JRNL REF NATURE V. 561 485 2018 JRNL REFN ESSN 1476-4687 JRNL PMID 30209393 JRNL DOI 10.1038/S41586-018-0509-0 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 11225 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1125 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 27.8825 - 4.1950 1.00 1342 148 0.1632 0.1786 REMARK 3 2 4.1950 - 3.3315 0.99 1278 148 0.1511 0.1943 REMARK 3 3 3.3315 - 2.9109 0.99 1289 146 0.1787 0.2082 REMARK 3 4 2.9109 - 2.6450 0.99 1273 140 0.2095 0.2816 REMARK 3 5 2.6450 - 2.4555 0.98 1245 142 0.2014 0.2873 REMARK 3 6 2.4555 - 2.3108 0.98 1273 137 0.1941 0.2560 REMARK 3 7 2.3108 - 2.1951 0.98 1250 137 0.1902 0.2290 REMARK 3 8 2.1951 - 2.0996 0.90 1150 127 0.1921 0.2872 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.88 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 1629 REMARK 3 ANGLE : 0.508 2228 REMARK 3 CHIRALITY : 0.042 275 REMARK 3 PLANARITY : 0.006 284 REMARK 3 DIHEDRAL : 11.138 956 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 6CZJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000232434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11237 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.02000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.02700 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 2.6.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.5, 2.1 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 18.33900 REMARK 290 SMTRY3 2 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 SER A 109 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 LYS A 32 CE NZ REMARK 470 LYS A 56 NZ REMARK 470 LYS A 60 CE NZ REMARK 470 GLU A 72 CG CD OE1 OE2 REMARK 470 LYS A 90 CE NZ REMARK 470 GLN A 106 CD OE1 NE2 REMARK 470 GLN A 108 CG CD OE1 NE2 REMARK 470 SER B 1 OG REMARK 470 GLN B 5 CG CD OE1 NE2 REMARK 470 GLU B 18 CG CD OE1 OE2 REMARK 470 LYS B 49 CG CD CE NZ REMARK 470 LYS B 90 CE NZ 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 328 O HOH A 378 2545 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 LYS A 32 -63.25 -143.21 REMARK 500 LYS B 32 -71.19 -135.65 REMARK 500 ASP B 84 -66.12 -133.33 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 SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 202 DBREF 6CZJ A 1 109 PDB 6CZJ 6CZJ 1 109 DBREF 6CZJ B 1 109 PDB 6CZJ 6CZJ 1 109 SEQRES 1 A 109 SER ALA LEU ALA GLN GLN LEU PRO GLY THR TRP LYS MET SEQRES 2 A 109 ASP VAL THR SER GLU ASP GLY VAL ARG THR THR GLY GLN SEQRES 3 A 109 MET HIS ILE GLN PRO LYS THR PRO THR THR MET ASP VAL SEQRES 4 A 109 THR LEU THR GLY THR HIS ALA ASP GLY LYS PRO PHE THR SEQRES 5 A 109 GLY GLN GLY LYS ILE THR VAL LYS THR PRO THR THR VAL SEQRES 6 A 109 ASP ILE THR VAL THR TYR GLU ASP GLY SER THR ALA THR SEQRES 7 A 109 GLY GLN LEU THR VAL ASP SER PRO THR GLN PHE LYS PHE SEQRES 8 A 109 ASP MET THR ALA SER ASP GLY THR ARG PHE THR GLY THR SEQRES 9 A 109 VAL GLN ARG GLN SER SEQRES 1 B 109 SER ALA LEU ALA GLN GLN LEU PRO GLY THR TRP LYS MET SEQRES 2 B 109 ASP VAL THR SER GLU ASP GLY VAL ARG THR THR GLY GLN SEQRES 3 B 109 MET HIS ILE GLN PRO LYS THR PRO THR THR MET ASP VAL SEQRES 4 B 109 THR LEU THR GLY THR HIS ALA ASP GLY LYS PRO PHE THR SEQRES 5 B 109 GLY GLN GLY LYS ILE THR VAL LYS THR PRO THR THR VAL SEQRES 6 B 109 ASP ILE THR VAL THR TYR GLU ASP GLY SER THR ALA THR SEQRES 7 B 109 GLY GLN LEU THR VAL ASP SER PRO THR GLN PHE LYS PHE SEQRES 8 B 109 ASP MET THR ALA SER ASP GLY THR ARG PHE THR GLY THR SEQRES 9 B 109 VAL GLN ARG GLN SER HET SO4 A 201 5 HET SO4 B 201 5 HET SO4 B 202 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 3(O4 S 2-) FORMUL 6 HOH *208(H2 O) HELIX 1 AA1 SER A 1 LEU A 7 1 7 HELIX 2 AA2 ALA B 2 LEU B 7 1 6 SHEET 1 AA1 9 GLY A 9 SER A 17 0 SHEET 2 AA1 9 ARG A 22 PRO A 31 -1 O GLY A 25 N MET A 13 SHEET 3 AA1 9 THR A 36 THR A 44 -1 O ASP A 38 N GLN A 30 SHEET 4 AA1 9 PRO A 50 VAL A 59 -1 O GLY A 53 N LEU A 41 SHEET 5 AA1 9 THR A 64 TYR A 71 -1 O ASP A 66 N THR A 58 SHEET 6 AA1 9 THR A 76 SER A 85 -1 O ALA A 77 N VAL A 69 SHEET 7 AA1 9 GLN A 88 ALA A 95 -1 O LYS A 90 N THR A 82 SHEET 8 AA1 9 ARG A 100 GLN A 108 -1 O PHE A 101 N MET A 93 SHEET 9 AA1 9 GLY A 9 SER A 17 -1 N LYS A 12 O GLN A 106 SHEET 1 AA2 9 GLY B 9 SER B 17 0 SHEET 2 AA2 9 ARG B 22 THR B 33 -1 O ILE B 29 N GLY B 9 SHEET 3 AA2 9 THR B 36 HIS B 45 -1 O THR B 40 N HIS B 28 SHEET 4 AA2 9 PRO B 50 VAL B 59 -1 O GLY B 53 N LEU B 41 SHEET 5 AA2 9 THR B 64 TYR B 71 -1 O ASP B 66 N THR B 58 SHEET 6 AA2 9 THR B 76 SER B 85 -1 O GLY B 79 N ILE B 67 SHEET 7 AA2 9 GLN B 88 ALA B 95 -1 O LYS B 90 N THR B 82 SHEET 8 AA2 9 ARG B 100 ARG B 107 -1 O PHE B 101 N MET B 93 SHEET 9 AA2 9 GLY B 9 SER B 17 -1 N LYS B 12 O GLN B 106 SITE 1 AC1 7 PRO A 50 PHE A 51 THR A 52 TYR A 71 SITE 2 AC1 7 GLU A 72 ASP A 73 HOH A 301 SITE 1 AC2 5 LYS A 12 GLN B 108 SER B 109 HOH B 302 SITE 2 AC2 5 HOH B 322 SITE 1 AC3 5 LYS B 32 THR B 33 THR B 36 LYS B 56 SITE 2 AC3 5 HOH B 301 CRYST1 42.915 36.678 61.912 90.00 91.08 90.00 P 1 21 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 0.023302 0.000000 0.000437 0.00000 SCALE2 0.000000 0.027264 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016155 0.00000