HEADER DE NOVO PROTEIN 21-FEB-23 8G9J TITLE GEOMETRICALLY PROGRAMMABLE NANOMATERIAL CONSTRUCTION USING REGULARIZED TITLE 2 PROTEIN BUILDING BLOCKS COMPND MOL_ID: 1; COMPND 2 MOLECULE: THR1; 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 KEYWDS NANOMATERIAL, PROTEIN BUILDING BLOCKS, DE NOVO DESIGN, TRAIN-TRACK, KEYWDS 2 DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.HUDDY,A.K.BERA,D.BAKER REVDAT 3 10-APR-24 8G9J 1 JRNL REVDAT 2 27-MAR-24 8G9J 1 JRNL REVDAT 1 13-MAR-24 8G9J 0 JRNL AUTH T.F.HUDDY,Y.HSIA,R.D.KIBLER,J.XU,N.BETHEL,D.NAGARAJAN, JRNL AUTH 2 R.REDLER,P.J.Y.LEUNG,C.WEIDLE,A.COURBET,E.C.YANG,A.K.BERA, JRNL AUTH 3 N.COUDRAY,S.J.CALISE,F.A.DAVILA-HERNANDEZ,H.L.HAN,K.D.CARR, JRNL AUTH 4 Z.LI,R.MCHUGH,G.REGGIANO,A.KANG,B.SANKARAN,M.S.DICKINSON, JRNL AUTH 5 B.COVENTRY,T.J.BRUNETTE,Y.LIU,J.DAUPARAS,A.J.BORST,D.EKIERT, JRNL AUTH 6 J.M.KOLLMAN,G.BHABHA,D.BAKER JRNL TITL BLUEPRINTING EXTENDABLE NANOMATERIALS WITH STANDARDIZED JRNL TITL 2 PROTEIN BLOCKS. JRNL REF NATURE V. 627 898 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 38480887 JRNL DOI 10.1038/S41586-024-07188-4 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_4761 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 6005 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.239 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 600 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 46.3900 - 3.9700 1.00 1455 163 0.1998 0.2184 REMARK 3 2 3.9700 - 3.1500 1.00 1353 148 0.2311 0.3215 REMARK 3 3 3.1500 - 2.7500 1.00 1334 148 0.2756 0.3635 REMARK 3 4 2.7500 - 2.5000 0.96 1263 141 0.2988 0.3763 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) : 0.304 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.628 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.66 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 : 0.003 1488 REMARK 3 ANGLE : 0.517 2011 REMARK 3 CHIRALITY : 0.031 263 REMARK 3 PLANARITY : 0.003 258 REMARK 3 DIHEDRAL : 20.740 567 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 8G9J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1000272420. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99993 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6005 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 46.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 1.700 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.30 REMARK 200 R MERGE FOR SHELL (I) : 0.43100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.59 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M BIS-TRIS PH 5.5, AND 25% W/V POLYETHYLENE GLYCOL 3,350, REMARK 280 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 64.63000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.85050 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.85050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.31500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.85050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.85050 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 96.94500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.85050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.85050 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.31500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.85050 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.85050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 96.94500 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 64.63000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A -12 REMARK 465 GLY A -11 REMARK 465 SER A -10 REMARK 465 GLY A -9 REMARK 465 GLU A -8 REMARK 465 ASN A -7 REMARK 465 LEU A -6 REMARK 465 TYR A -5 REMARK 465 PHE A -4 REMARK 465 GLN A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 GLY A 0 REMARK 465 GLY A 202 REMARK 465 ALA A 203 REMARK 465 SER A 204 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 ALA A 152 -151.79 55.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 8G9J A -18 204 PDB 8G9J 8G9J -18 204 SEQRES 1 A 223 HIS HIS HIS HIS HIS HIS SER GLY SER GLY GLU ASN LEU SEQRES 2 A 223 TYR PHE GLN GLY SER GLY SER GLU GLU ILE VAL GLU GLU SEQRES 3 A 223 ALA GLU THR ALA LEU LYS ALA LEU LEU GLU GLU ALA GLU SEQRES 4 A 223 LYS GLY GLY LYS GLU ASP ALA LEU GLU ILE ALA GLU LYS SEQRES 5 A 223 LEU ALA GLU LEU ALA LYS GLU ALA LEU GLU VAL LEU LEU SEQRES 6 A 223 GLU ALA GLY ALA SER PRO GLU LEU ILE VAL ARG LEU ALA SEQRES 7 A 223 GLU THR ALA LEU LYS ALA LEU LEU ALA ILE ALA GLU LEU SEQRES 8 A 223 GLY GLY GLU GLU LEU ALA LEU GLU ILE ALA ARG ILE LEU SEQRES 9 A 223 ALA GLU LEU ALA GLU VAL ALA LEU GLU VAL LEU LEU GLU SEQRES 10 A 223 LEU GLY ALA SER PRO GLU LEU ILE VAL ARG LEU ALA GLU SEQRES 11 A 223 THR ALA LEU GLU ALA LEU LEU ALA ILE ALA ARG LEU GLY SEQRES 12 A 223 GLY GLU GLU LEU ALA LEU GLU ILE ALA ARG ILE LEU ALA SEQRES 13 A 223 GLU LEU ALA GLU VAL ALA LEU GLU VAL LEU LEU GLU LEU SEQRES 14 A 223 GLY ALA SER PRO GLU LEU ILE LYS LYS LEU ALA GLU THR SEQRES 15 A 223 ALA GLU GLU ALA LEU GLU ALA ILE ALA LYS LEU GLY GLY SEQRES 16 A 223 GLU GLU LEU ALA GLU GLU ILE ALA LYS ILE LEU ALA GLU SEQRES 17 A 223 LEU ALA GLU VAL ALA LYS GLU VAL GLN LYS GLU LEU GLY SEQRES 18 A 223 ALA SER FORMUL 2 HOH *13(H2 O) HELIX 1 AA1 SER A 1 GLY A 22 1 22 HELIX 2 AA2 GLY A 23 ALA A 48 1 26 HELIX 3 AA3 SER A 51 GLY A 73 1 23 HELIX 4 AA4 GLY A 74 LEU A 99 1 26 HELIX 5 AA5 SER A 102 GLY A 124 1 23 HELIX 6 AA6 GLY A 125 LEU A 150 1 26 HELIX 7 AA7 SER A 153 LYS A 173 1 21 HELIX 8 AA8 GLY A 176 GLU A 200 1 25 CRYST1 49.701 49.701 129.260 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 0.020120 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007736 0.00000