HEADER DE NOVO PROTEIN 11-FEB-19 6NYI TITLE CRYSTAL STRUCTURE OF COMPUTATIONALLY DESIGNED PROTEIN XXA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGN CONSTRUCT XXA; 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 6NYI 1 REMARK REVDAT 1 22-APR-20 6NYI 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 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 63.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 REMARK 3 NUMBER OF REFLECTIONS : 12952 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.261 REMARK 3 R VALUE (WORKING SET) : 0.259 REMARK 3 FREE R VALUE : 0.281 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1312 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 63.2046 - 4.7837 0.98 1419 161 0.2412 0.2611 REMARK 3 2 4.7837 - 3.7971 0.98 1398 157 0.1953 0.2204 REMARK 3 3 3.7971 - 3.3171 0.97 1358 151 0.2367 0.2568 REMARK 3 4 3.3171 - 3.0139 0.96 1335 151 0.2698 0.2947 REMARK 3 5 3.0139 - 2.7978 0.92 1303 144 0.2730 0.2881 REMARK 3 6 2.7978 - 2.6329 0.90 1238 148 0.3069 0.3397 REMARK 3 7 2.6329 - 2.5010 0.88 1239 138 0.3251 0.3315 REMARK 3 8 2.5010 - 2.3921 0.87 1211 137 0.3520 0.4478 REMARK 3 9 2.3921 - 2.3001 0.82 1139 125 0.4290 0.4410 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) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 35.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 56.52 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 6NYI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1000239664. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : 16412 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.170 REMARK 200 RESOLUTION RANGE LOW (A) : 63.181 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.15500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.22800 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.16 M MAGNESIUM ACETATE, 0.08 M REMARK 280 SODIUM CACODYLATE PH 6.5, 20% (V/V) GLYCEROL, VAPOR DIFFUSION, REMARK 280 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 64.70150 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.60650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 64.70150 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.60650 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: 8580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.0 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 75 REMARK 465 GLY B 75 REMARK 465 GLU B 94 REMARK 465 ARG B 95 REMARK 465 GLY B 96 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 HIS C 1 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 ARG A 13 CD NE CZ NH1 NH2 REMARK 470 GLU A 19 OE1 OE2 REMARK 470 ARG A 20 NE CZ NH1 NH2 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 ARG A 35 CD NE CZ NH1 NH2 REMARK 470 ARG A 49 CD NE CZ NH1 NH2 REMARK 470 LYS A 77 CG CD CE NZ REMARK 470 GLU A 81 CD OE1 OE2 REMARK 470 LYS A 87 CD CE NZ REMARK 470 GLU B 12 CD OE1 OE2 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 GLU B 27 CD OE1 OE2 REMARK 470 LYS B 28 CG CD CE NZ REMARK 470 GLN B 29 CG CD OE1 NE2 REMARK 470 GLU B 39 CG CD OE1 OE2 REMARK 470 ARG B 49 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 53 CD OE1 OE2 REMARK 470 LYS B 77 CG CD CE NZ REMARK 470 LEU B 79 CD1 CD2 REMARK 470 GLU B 80 CG CD OE1 OE2 REMARK 470 GLU B 81 CD OE1 OE2 REMARK 470 LYS B 83 NZ REMARK 470 LYS B 84 CG CD CE NZ REMARK 470 LYS B 87 CD CE NZ REMARK 470 LYS B 90 CD CE NZ REMARK 470 ARG B 91 CG CD NE CZ NH1 NH2 REMARK 470 LEU B 93 CG CD1 CD2 REMARK 470 MET C 2 CG SD CE REMARK 470 GLU C 5 CG CD OE1 OE2 REMARK 470 LYS C 8 CD CE NZ REMARK 470 TYR C 9 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU C 12 CG CD OE1 OE2 REMARK 470 ARG C 13 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 16 CG CD OE1 OE2 REMARK 470 GLU C 19 CG CD OE1 OE2 REMARK 470 GLU C 23 CD OE1 OE2 REMARK 470 ASN C 24 CG OD1 ND2 REMARK 470 LYS C 28 CD CE NZ REMARK 470 GLN C 29 CD OE1 NE2 REMARK 470 GLU C 32 CD OE1 OE2 REMARK 470 GLU C 39 CD OE1 OE2 REMARK 470 GLU C 46 CD OE1 OE2 REMARK 470 ARG C 49 CD NE CZ NH1 NH2 REMARK 470 LYS C 77 CG CD CE NZ REMARK 470 ILE C 78 CG1 CG2 CD1 REMARK 470 GLU C 80 CD OE1 OE2 REMARK 470 GLU C 81 CG CD OE1 OE2 REMARK 470 LYS C 84 CD CE NZ REMARK 470 ARG C 91 NE CZ NH1 NH2 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 SER A 26 147.52 -175.54 REMARK 500 PRO C 25 107.90 -51.96 REMARK 500 REMARK 500 REMARK: NULL DBREF 6NYI A -1 96 PDB 6NYI 6NYI -1 96 DBREF 6NYI B -1 96 PDB 6NYI 6NYI -1 96 DBREF 6NYI C -1 96 PDB 6NYI 6NYI -1 96 SEQRES 1 A 98 GLY SER HIS MET GLY THR GLU ASP LEU LYS TYR SER LEU SEQRES 2 A 98 GLU ARG LEU ARG GLU ILE LEU GLU ARG LEU GLU GLU ASN SEQRES 3 A 98 PRO SER GLU LYS GLN ILE VAL GLU ALA ILE ARG ALA ILE SEQRES 4 A 98 VAL GLU ASN ASN ALA GLN ILE VAL GLU ALA ILE ARG ALA SEQRES 5 A 98 ILE VAL GLU ASN ASN ALA GLN ILE VAL GLU ILE LEU ARG SEQRES 6 A 98 ALA ILE ILE GLU ALA LEU GLU ALA ILE GLY GLY GLY THR SEQRES 7 A 98 LYS ILE LEU GLU GLU MET LYS LYS LEU LEU LYS ASP LEU SEQRES 8 A 98 LYS ARG SER LEU GLU ARG GLY SEQRES 1 B 98 GLY SER HIS MET GLY THR GLU ASP LEU LYS TYR SER LEU SEQRES 2 B 98 GLU ARG LEU ARG GLU ILE LEU GLU ARG LEU GLU GLU ASN SEQRES 3 B 98 PRO SER GLU LYS GLN ILE VAL GLU ALA ILE ARG ALA ILE SEQRES 4 B 98 VAL GLU ASN ASN ALA GLN ILE VAL GLU ALA ILE ARG ALA SEQRES 5 B 98 ILE VAL GLU ASN ASN ALA GLN ILE VAL GLU ILE LEU ARG SEQRES 6 B 98 ALA ILE ILE GLU ALA LEU GLU ALA ILE GLY GLY GLY THR SEQRES 7 B 98 LYS ILE LEU GLU GLU MET LYS LYS LEU LEU LYS ASP LEU SEQRES 8 B 98 LYS ARG SER LEU GLU ARG GLY SEQRES 1 C 98 GLY SER HIS MET GLY THR GLU ASP LEU LYS TYR SER LEU SEQRES 2 C 98 GLU ARG LEU ARG GLU ILE LEU GLU ARG LEU GLU GLU ASN SEQRES 3 C 98 PRO SER GLU LYS GLN ILE VAL GLU ALA ILE ARG ALA ILE SEQRES 4 C 98 VAL GLU ASN ASN ALA GLN ILE VAL GLU ALA ILE ARG ALA SEQRES 5 C 98 ILE VAL GLU ASN ASN ALA GLN ILE VAL GLU ILE LEU ARG SEQRES 6 C 98 ALA ILE ILE GLU ALA LEU GLU ALA ILE GLY GLY GLY THR SEQRES 7 C 98 LYS ILE LEU GLU GLU MET LYS LYS LEU LEU LYS ASP LEU SEQRES 8 C 98 LYS ARG SER LEU GLU ARG GLY FORMUL 4 HOH *30(H2 O) HELIX 1 AA1 GLY A 3 ASN A 24 1 22 HELIX 2 AA2 SER A 26 GLY A 74 1 49 HELIX 3 AA3 LYS A 77 SER A 92 1 16 HELIX 4 AA4 GLY B 3 ASN B 24 1 22 HELIX 5 AA5 SER B 26 GLY B 74 1 49 HELIX 6 AA6 LYS B 77 LEU B 93 1 17 HELIX 7 AA7 THR C 4 ASN C 24 1 21 HELIX 8 AA8 SER C 26 GLY C 74 1 49 HELIX 9 AA9 THR C 76 LEU C 93 1 18 CRYST1 129.403 51.213 48.838 90.00 102.45 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 0.007728 0.000000 0.001706 0.00000 SCALE2 0.000000 0.019526 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020969 0.00000