HEADER DE NOVO PROTEIN 12-FEB-19 6NZ3 TITLE CRYSTAL STRUCTURE OF COMPUTATIONALLY DESIGNED PROTEIN XAA_GGHN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGN CONSTRUCT XAA_GGHN; COMPND 3 CHAIN: A, B, C; 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 HOMOTRIMER, HELIX, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.Y.WEI,M.J.BICK REVDAT 2 13-MAR-24 6NZ3 1 REMARK REVDAT 1 22-APR-20 6NZ3 0 JRNL AUTH K.Y.WEI,D.MOSCHIDI,M.J.BICK,S.NERLI,A.C.MCSHAN,L.P.CARTER, JRNL AUTH 2 P.S.HUANG,D.A.FLETCHER,N.G.SGOURAKIS,S.E.BOYKEN,D.BAKER JRNL TITL COMPUTATIONAL DESIGN OF CLOSELY RELATED PROTEINS THAT ADOPT JRNL TITL 2 TWO WELL-DEFINED BUT STRUCTURALLY DIVERGENT FOLDS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 117 7208 2020 JRNL REFN ESSN 1091-6490 JRNL PMID 32188784 JRNL DOI 10.1073/PNAS.1914808117 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 80.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 16014 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.264 REMARK 3 R VALUE (WORKING SET) : 0.262 REMARK 3 FREE R VALUE : 0.302 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.760 REMARK 3 FREE R VALUE TEST SET COUNT : 922 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 80.7048 - 4.3995 0.97 2215 132 0.2564 0.3102 REMARK 3 2 4.3995 - 3.4920 1.00 2192 142 0.2339 0.2530 REMARK 3 3 3.4920 - 3.0506 0.99 2156 130 0.2847 0.3013 REMARK 3 4 3.0506 - 2.7716 0.99 2181 126 0.2926 0.3478 REMARK 3 5 2.7716 - 2.5730 0.98 2122 130 0.2995 0.3953 REMARK 3 6 2.5730 - 2.4213 0.97 2138 127 0.2764 0.3548 REMARK 3 7 2.4213 - 2.3000 0.96 2088 135 0.2586 0.2913 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.40 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6NZ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1000239707. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1111 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34486 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 80.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.03500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.66 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 23.6 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 : 0.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CAPS PH 10.5, 40% (V/V) MPD, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K 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 44.37050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.63550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.37050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.63550 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -110.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 1 REMARK 465 GLU A 94 REMARK 465 ARG A 95 REMARK 465 GLY A 96 REMARK 465 GLY B 1 REMARK 465 SER B 2 REMARK 465 GLU B 94 REMARK 465 ARG B 95 REMARK 465 GLY B 96 REMARK 465 GLY C 1 REMARK 465 GLU C 94 REMARK 465 ARG C 95 REMARK 465 GLY C 96 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 SER A 2 OG REMARK 470 LYS A 8 CD CE NZ REMARK 470 ARG A 13 CD NE CZ NH1 NH2 REMARK 470 GLU A 19 CG CD OE1 OE2 REMARK 470 GLU A 23 CG CD OE1 OE2 REMARK 470 ASN A 24 CG OD1 ND2 REMARK 470 LYS A 28 CG CD CE NZ REMARK 470 LYS A 77 CG CD CE NZ REMARK 470 GLU A 80 CD OE1 OE2 REMARK 470 GLU A 81 OE1 OE2 REMARK 470 LYS A 83 CG CD CE NZ REMARK 470 LYS A 84 CG CD CE NZ REMARK 470 GLN A 85 CD OE1 NE2 REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 LYS A 90 CE NZ REMARK 470 ARG A 91 NE CZ NH1 NH2 REMARK 470 LEU A 93 CG CD1 CD2 REMARK 470 LYS B 8 CD CE NZ REMARK 470 GLU B 12 CG CD OE1 OE2 REMARK 470 ARG B 13 NE CZ NH1 NH2 REMARK 470 GLU B 19 CG CD OE1 OE2 REMARK 470 GLU B 23 CG CD OE1 OE2 REMARK 470 ASN B 24 CG OD1 ND2 REMARK 470 LYS B 28 CG CD CE NZ REMARK 470 LYS B 77 CG CD CE NZ REMARK 470 GLU B 80 CD OE1 OE2 REMARK 470 GLU B 81 CD OE1 OE2 REMARK 470 LYS B 83 CG CD CE NZ REMARK 470 LYS B 84 CD CE NZ REMARK 470 GLN B 85 CD OE1 NE2 REMARK 470 LYS B 87 CE NZ REMARK 470 ASP B 88 OD1 OD2 REMARK 470 LYS B 90 CD CE NZ REMARK 470 ARG B 91 CD NE CZ NH1 NH2 REMARK 470 SER C 2 OG REMARK 470 MET C 4 CE REMARK 470 LYS C 8 CD CE NZ REMARK 470 GLU C 12 CG CD OE1 OE2 REMARK 470 ARG C 13 NE CZ NH1 NH2 REMARK 470 GLU C 16 CD OE1 OE2 REMARK 470 GLU C 19 CG CD OE1 OE2 REMARK 470 GLU C 23 CG CD OE1 OE2 REMARK 470 ASN C 24 CG OD1 ND2 REMARK 470 LYS C 28 CG CD CE NZ REMARK 470 LYS C 77 CG CD CE NZ REMARK 470 GLU C 80 CD OE1 OE2 REMARK 470 LYS C 83 CG CD CE NZ REMARK 470 LYS C 84 CG CD CE NZ REMARK 470 GLN C 85 CD OE1 NE2 REMARK 470 LYS C 87 CG CD CE NZ REMARK 470 ASP C 88 OD1 OD2 REMARK 470 LYS C 90 CD CE NZ REMARK 470 ARG C 91 CD NE CZ NH1 NH2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 101 DBREF 6NZ3 A 1 96 PDB 6NZ3 6NZ3 1 96 DBREF 6NZ3 B 1 96 PDB 6NZ3 6NZ3 1 96 DBREF 6NZ3 C 1 96 PDB 6NZ3 6NZ3 1 96 SEQRES 1 A 96 GLY SER HIS MET GLY ASP LEU LYS TYR SER LEU GLU ARG SEQRES 2 A 96 LEU ARG GLU ILE LEU GLU ARG LEU GLU GLU ASN PRO SER SEQRES 3 A 96 GLU LYS GLN ILE VAL GLU ALA ILE ARG ALA ILE VAL GLU SEQRES 4 A 96 ASN ASN ALA GLN ILE VAL GLU ALA ILE ARG ALA ILE VAL SEQRES 5 A 96 GLU ASN ASN ALA GLN ILE VAL GLU ASN ASN ARG ALA ILE SEQRES 6 A 96 ILE GLU ALA LEU GLU ALA ILE GLY GLY HIS ASN LYS ILE SEQRES 7 A 96 LEU GLU GLU MET LYS LYS GLN LEU LYS ASP LEU LYS ARG SEQRES 8 A 96 SER LEU GLU ARG GLY SEQRES 1 B 96 GLY SER HIS MET GLY ASP LEU LYS TYR SER LEU GLU ARG SEQRES 2 B 96 LEU ARG GLU ILE LEU GLU ARG LEU GLU GLU ASN PRO SER SEQRES 3 B 96 GLU LYS GLN ILE VAL GLU ALA ILE ARG ALA ILE VAL GLU SEQRES 4 B 96 ASN ASN ALA GLN ILE VAL GLU ALA ILE ARG ALA ILE VAL SEQRES 5 B 96 GLU ASN ASN ALA GLN ILE VAL GLU ASN ASN ARG ALA ILE SEQRES 6 B 96 ILE GLU ALA LEU GLU ALA ILE GLY GLY HIS ASN LYS ILE SEQRES 7 B 96 LEU GLU GLU MET LYS LYS GLN LEU LYS ASP LEU LYS ARG SEQRES 8 B 96 SER LEU GLU ARG GLY SEQRES 1 C 96 GLY SER HIS MET GLY ASP LEU LYS TYR SER LEU GLU ARG SEQRES 2 C 96 LEU ARG GLU ILE LEU GLU ARG LEU GLU GLU ASN PRO SER SEQRES 3 C 96 GLU LYS GLN ILE VAL GLU ALA ILE ARG ALA ILE VAL GLU SEQRES 4 C 96 ASN ASN ALA GLN ILE VAL GLU ALA ILE ARG ALA ILE VAL SEQRES 5 C 96 GLU ASN ASN ALA GLN ILE VAL GLU ASN ASN ARG ALA ILE SEQRES 6 C 96 ILE GLU ALA LEU GLU ALA ILE GLY GLY HIS ASN LYS ILE SEQRES 7 C 96 LEU GLU GLU MET LYS LYS GLN LEU LYS ASP LEU LYS ARG SEQRES 8 C 96 SER LEU GLU ARG GLY HET CL A 101 1 HETNAM CL CHLORIDE ION FORMUL 4 CL CL 1- FORMUL 5 HOH *10(H2 O) HELIX 1 AA1 SER A 2 ASN A 24 1 23 HELIX 2 AA2 SER A 26 LEU A 93 1 68 HELIX 3 AA3 MET B 4 ASN B 24 1 21 HELIX 4 AA4 SER B 26 LEU B 93 1 68 HELIX 5 AA5 HIS C 3 ASN C 24 1 22 HELIX 6 AA6 SER C 26 LEU C 93 1 68 SITE 1 AC1 3 ASN A 61 ASN B 61 ASN C 61 CRYST1 88.741 51.271 85.873 90.00 110.08 90.00 C 1 2 1 12 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 0.011269 0.000000 0.004118 0.00000 SCALE2 0.000000 0.019504 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012398 0.00000