HEADER DE NOVO PROTEIN 14-OCT-23 8UKM TITLE T33-ML30 - DESIGNED TETRAHEDRAL PROTEIN CAGE USING MACHINE LEARNING TITLE 2 ALGORITHMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: T33-ML30-REDESIGNED-TANDEM-BMC-T-FOLD; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: T33-ML30-REDESIGNED-4-OT-FOLD; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: LOBSTR; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PSAM; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 13 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: LOBSTR; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: PSAM KEYWDS NANOHEDRA, PROTEIN CAGE, TETRAHEDRAL, DE NOVO PROTEIN INTERFACE, KEYWDS 2 MACHINE LEARNING, TWO COMPONENTS, PROTEINMPNN, NANOPARTICLE, DE NOVO KEYWDS 3 PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR R.CASTELLS-GRAELLS,K.MEADOR,M.R.SAWAYA,T.O.YEATES REVDAT 2 03-APR-24 8UKM 1 JRNL REVDAT 1 06-MAR-24 8UKM 0 JRNL AUTH K.MEADOR,R.CASTELLS-GRAELLS,R.AGUIRRE,M.R.SAWAYA,M.A.ARBING, JRNL AUTH 2 T.SHERMAN,C.SENARATHNE,T.O.YEATES JRNL TITL A SUITE OF DESIGNED PROTEIN CAGES USING MACHINE LEARNING AND JRNL TITL 2 PROTEIN FRAGMENT-BASED PROTOCOLS. JRNL REF STRUCTURE 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 38513658 JRNL DOI 10.1016/J.STR.2024.02.017 REMARK 2 REMARK 2 RESOLUTION. 4.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.200 REMARK 3 NUMBER OF PARTICLES : 7114 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8UKM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000278172. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : T33-ML30 DESIGNED TETRAHEDRAL REMARK 245 PROTEIN CAGE USING MACHINE REMARK 245 LEARNING REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 500.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 4750.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: 24-MERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 350 BIOMT1 2 -0.500005 -0.866033 0.000000 286.29054 REMARK 350 BIOMT2 2 0.866033 -0.500004 0.000000 76.71052 REMARK 350 BIOMT3 2 0.000000 0.000000 0.999999 0.00011 REMARK 350 BIOMT1 3 -0.500005 0.866033 0.000000 76.71056 REMARK 350 BIOMT2 3 -0.866033 -0.500004 0.000000 286.29050 REMARK 350 BIOMT3 3 0.000000 0.000000 0.999999 0.00011 REMARK 350 BIOMT1 4 0.000000 0.577355 -0.816500 149.93650 REMARK 350 BIOMT2 4 0.577355 -0.666672 -0.471406 188.84751 REMARK 350 BIOMT3 4 -0.816500 -0.471406 -0.333333 317.16994 REMARK 350 BIOMT1 5 0.500005 -0.288678 -0.816500 194.22594 REMARK 350 BIOMT2 5 -0.866033 -0.166668 -0.471406 302.99698 REMARK 350 BIOMT3 5 0.000000 0.942813 -0.333333 47.25298 REMARK 350 BIOMT1 6 -0.500005 -0.288678 -0.816500 315.22704 REMARK 350 BIOMT2 6 0.288678 0.833340 -0.471406 42.27598 REMARK 350 BIOMT3 6 0.816500 -0.471406 -0.333333 119.57697 REMARK 350 BIOMT1 7 0.000000 -0.577355 0.816500 92.06350 REMARK 350 BIOMT2 7 -0.577355 -0.666672 -0.471406 328.56750 REMARK 350 BIOMT3 7 0.816500 -0.471406 -0.333333 119.57697 REMARK 350 BIOMT1 8 -0.500005 0.288678 0.816500 47.77406 REMARK 350 BIOMT2 8 -0.288678 0.833340 -0.471406 112.13598 REMARK 350 BIOMT3 8 -0.816500 -0.471406 -0.333333 317.16994 REMARK 350 BIOMT1 9 0.500005 0.288678 0.816500 -73.22704 REMARK 350 BIOMT2 9 0.866033 -0.166668 -0.471406 93.41701 REMARK 350 BIOMT3 9 0.000000 0.942813 -0.333333 47.25298 REMARK 350 BIOMT1 10 -1.000009 0.000000 0.000000 242.00110 REMARK 350 BIOMT2 10 0.000000 0.333336 0.942813 -33.41399 REMARK 350 BIOMT3 10 0.000000 0.942813 -0.333333 47.25298 REMARK 350 BIOMT1 11 0.500005 0.866033 0.000000 -44.29054 REMARK 350 BIOMT2 11 0.288678 -0.166668 0.942813 -7.84348 REMARK 350 BIOMT3 11 0.816500 -0.471406 -0.333333 119.57697 REMARK 350 BIOMT1 12 0.500005 -0.866033 0.000000 165.28944 REMARK 350 BIOMT2 12 -0.288678 -0.166668 0.942813 62.01651 REMARK 350 BIOMT3 12 -0.816500 -0.471406 -0.333333 317.16994 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 12 REMARK 465 GLY A 13 REMARK 465 PRO A 14 REMARK 465 ASP A 15 REMARK 465 GLU A 16 REMARK 465 PRO A 17 REMARK 465 GLU A 18 REMARK 465 PHE A 204 REMARK 465 PHE A 205 REMARK 465 MET B 1 REMARK 465 PRO B 2 REMARK 465 GLY B 112 REMARK 465 VAL B 113 REMARK 465 GLY B 114 REMARK 465 ASN B 115 REMARK 465 GLY B 116 REMARK 465 LYS B 117 REMARK 465 THR B 118 REMARK 465 ALA B 119 REMARK 465 ALA B 120 REMARK 465 GLU B 121 REMARK 465 ALA B 122 REMARK 465 GLY B 123 REMARK 465 GLY B 124 REMARK 465 SER B 125 REMARK 465 HIS B 126 REMARK 465 HIS B 127 REMARK 465 TRP B 128 REMARK 465 GLY B 129 REMARK 465 GLY B 130 REMARK 465 HIS B 131 REMARK 465 HIS B 132 REMARK 465 HIS B 133 REMARK 465 HIS B 134 REMARK 465 HIS B 135 REMARK 465 HIS B 136 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 PRO A 45 47.35 -84.97 REMARK 500 PRO A 56 45.97 -94.35 REMARK 500 VAL A 148 -62.99 -123.68 REMARK 500 SER A 153 15.61 55.61 REMARK 500 GLU B 70 -178.12 -68.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-42355 RELATED DB: EMDB REMARK 900 T33-ML30 - DESIGNED TETRAHEDRAL PROTEIN CAGE USING MACHINE LEARNING REMARK 900 ALGORITHMS DBREF 8UKM A 12 205 PDB 8UKM 8UKM 12 205 DBREF 8UKM B 1 136 PDB 8UKM 8UKM 1 136 SEQRES 1 A 194 MET GLY PRO ASP GLU PRO GLU ARG PRO ALA LEU LEU ILE SEQRES 2 A 194 LEU GLU LEU LYS SER TYR ALA ARG GLY VAL ARG VAL ALA SEQRES 3 A 194 ASP ALA ALA LEU LYS ALA ALA PRO VAL ARG LEU LEU LYS SEQRES 4 A 194 CYS LYS ILE VAL GLU PRO GLY LYS ALA LEU ILE MET LEU SEQRES 5 A 194 THR GLY ARG PRO GLU ASP VAL GLU LYS ALA TYR LYS ALA SEQRES 6 A 194 ALA LEU THR VAL ALA ASN LYS GLY SER GLY ASN LEU ILE SEQRES 7 A 194 ASP SER VAL PHE ILE PRO ALA ILE HIS PRO ALA LEU LEU SEQRES 8 A 194 PRO PHE LEU LEU GLU GLU THR PRO ALA PRO PRO LEU GLU SEQRES 9 A 194 ASP PRO ASP ARG ALA LEU LEU PHE VAL GLU VAL LYS THR SEQRES 10 A 194 VAL ALA ALA ALA ILE ARG ALA ALA ASP ALA ALA LEU ARG SEQRES 11 A 194 ALA ALA PRO VAL GLU LEU VAL ARG MET ARG LEU SER GLU SEQRES 12 A 194 HIS ILE GLY GLY LYS ALA VAL PHE ALA LEU VAL GLY ASP SEQRES 13 A 194 PRO ALA ASP VAL LEU ARG ALA ALA ALA VAL VAL ALA GLU SEQRES 14 A 194 VAL ALA GLY ASP GLN LEU LEU ASP ILE ALA ILE ILE PRO SEQRES 15 A 194 ARG PRO HIS PRO ALA LEU LEU GLY ARG GLU PHE PHE SEQRES 1 B 136 MET PRO MET LEU VAL VAL TYR VAL PRO GLU GLY TYR SER SEQRES 2 B 136 GLU ALA GLN LYS ARG ALA LEU LEU PHE ARG LEU ALA ALA SEQRES 3 B 136 ALA VAL VAL GLU ALA THR GLY THR PRO LEU GLU ASN VAL SEQRES 4 B 136 ARG ILE ILE LEU THR THR TYR ALA PRO ALA ASP VAL LEU SEQRES 5 B 136 LEU GLY GLY ALA ILE GLY VAL PRO LEU VAL VAL ILE LEU SEQRES 6 B 136 VAL TYR LEU LEU GLU GLY LEU SER PRO GLU GLN LYS ALA SEQRES 7 B 136 ALA LEU VAL LYS ALA LEU THR ALA ALA ALA ALA GLU ALA SEQRES 8 B 136 LEU GLY VAL ASP PRO GLU ASN ILE ARG VAL ILE LEU VAL SEQRES 9 B 136 PRO VAL PRO PRO GLU ASN PHE GLY VAL GLY ASN GLY LYS SEQRES 10 B 136 THR ALA ALA GLU ALA GLY GLY SER HIS HIS TRP GLY GLY SEQRES 11 B 136 HIS HIS HIS HIS HIS HIS HELIX 1 AA1 SER A 29 ALA A 44 1 16 HELIX 2 AA2 ARG A 66 ASN A 82 1 17 HELIX 3 AA3 ALA A 100 GLU A 107 1 8 HELIX 4 AA4 THR A 128 ALA A 143 1 16 HELIX 5 AA5 ASP A 167 GLY A 183 1 17 HELIX 6 AA6 SER B 13 GLY B 33 1 21 HELIX 7 AA7 PRO B 35 VAL B 39 5 5 HELIX 8 AA8 ALA B 47 ASP B 50 5 4 HELIX 9 AA9 SER B 73 GLY B 93 1 21 HELIX 10 AB1 ASP B 95 GLU B 97 5 3 SHEET 1 AA1 4 ARG A 47 VAL A 54 0 SHEET 2 AA1 4 LYS A 58 THR A 64 -1 O LEU A 60 N LYS A 52 SHEET 3 AA1 4 LEU A 22 LEU A 27 -1 N LEU A 27 O ALA A 59 SHEET 4 AA1 4 LEU A 88 ILE A 94 -1 O ILE A 94 N LEU A 22 SHEET 1 AA2 4 GLU A 146 LEU A 152 0 SHEET 2 AA2 4 ALA A 160 GLY A 166 -1 O ALA A 163 N ARG A 149 SHEET 3 AA2 4 ALA A 120 VAL A 126 -1 N LEU A 122 O LEU A 164 SHEET 4 AA2 4 LEU A 186 ILE A 192 -1 O LEU A 187 N GLU A 125 SHEET 1 AA3 4 ILE B 42 TYR B 46 0 SHEET 2 AA3 4 LEU B 4 PRO B 9 1 N VAL B 6 O THR B 44 SHEET 3 AA3 4 VAL B 62 LEU B 69 -1 O LEU B 65 N VAL B 5 SHEET 4 AA3 4 ILE B 99 VAL B 106 1 O ARG B 100 N ILE B 64 SHEET 1 AA4 2 LEU B 52 LEU B 53 0 SHEET 2 AA4 2 ALA B 56 ILE B 57 -1 O ALA B 56 N LEU B 53 CISPEP 1 GLU A 55 PRO A 56 0 0.44 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000