HEADER DE NOVO PROTEIN 18-OCT-23 8UMP TITLE T33-ML35 - DESIGNED TETRAHEDRAL PROTEIN CAGE USING MACHINE LEARNING TITLE 2 ALGORITHMS COMPND MOL_ID: 1; COMPND 2 MOLECULE: T33-ML35-REDESIGNED-TPR-DOMAIN-FOLD; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: T33-ML35-REDESIGNED-CUTA-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 8UMP 1 JRNL REVDAT 1 15-NOV-23 8UMP 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. 2.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : PHENIX, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL 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) : 2.920 REMARK 3 NUMBER OF PARTICLES : 54116 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 8UMP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-23. REMARK 100 THE DEPOSITION ID IS D_1000278419. 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-ML35 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 : 7.50 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) : 4000.00 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: DIMERIC 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 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 -0.500005 -0.866033 0.000000 246.06790 REMARK 350 BIOMT2 2 0.866033 -0.500004 0.000000 65.93301 REMARK 350 BIOMT3 2 0.000000 0.000000 0.999999 0.00010 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 3 -0.500005 0.866033 0.000000 65.93304 REMARK 350 BIOMT2 3 -0.866033 -0.500004 0.000000 246.06787 REMARK 350 BIOMT3 3 0.000000 0.000000 0.999999 0.00010 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 4 0.000000 0.577355 -0.816500 128.87104 REMARK 350 BIOMT2 4 0.577355 -0.666672 -0.471406 162.31521 REMARK 350 BIOMT3 4 -0.816500 -0.471406 -0.333333 272.60888 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 5 0.500005 -0.288678 -0.816500 166.93799 REMARK 350 BIOMT2 5 -0.866033 -0.166668 -0.471406 260.42716 REMARK 350 BIOMT3 5 0.000000 0.942813 -0.333333 40.61413 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 6 -0.500005 -0.288678 -0.816500 270.93894 REMARK 350 BIOMT2 6 0.288678 0.833340 -0.471406 36.33638 REMARK 350 BIOMT3 6 0.816500 -0.471406 -0.333333 102.77690 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 7 0.000000 -0.577355 0.816500 79.12896 REMARK 350 BIOMT2 7 -0.577355 -0.666672 -0.471406 282.40512 REMARK 350 BIOMT3 7 0.816500 -0.471406 -0.333333 102.77690 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 8 -0.500005 0.288678 0.816500 41.06201 REMARK 350 BIOMT2 8 -0.288678 0.833340 -0.471406 96.38134 REMARK 350 BIOMT3 8 -0.816500 -0.471406 -0.333333 272.60888 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 9 0.500005 0.288678 0.816500 -62.93894 REMARK 350 BIOMT2 9 0.866033 -0.166668 -0.471406 80.29230 REMARK 350 BIOMT3 9 0.000000 0.942813 -0.333333 40.61413 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 10 -1.000009 0.000000 0.000000 208.00095 REMARK 350 BIOMT2 10 0.000000 0.333336 0.942813 -28.71946 REMARK 350 BIOMT3 10 0.000000 0.942813 -0.333333 40.61413 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 11 0.500005 0.866033 0.000000 -38.06790 REMARK 350 BIOMT2 11 0.288678 -0.166668 0.942813 -6.74150 REMARK 350 BIOMT3 11 0.816500 -0.471406 -0.333333 102.77690 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 12 0.500005 -0.866033 0.000000 142.06696 REMARK 350 BIOMT2 12 -0.288678 -0.166668 0.942813 53.30345 REMARK 350 BIOMT3 12 -0.816500 -0.471406 -0.333333 272.60888 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 1 REMARK 465 GLU A 122 REMARK 465 MET B 11 REMARK 465 THR B 12 REMARK 465 ASP B 13 REMARK 465 LEU B 14 REMARK 465 SER B 15 REMARK 465 GLN B 123 REMARK 465 GLY B 124 REMARK 465 GLY B 125 REMARK 465 SER B 126 REMARK 465 HIS B 127 REMARK 465 HIS B 128 REMARK 465 TRP B 129 REMARK 465 GLY B 130 REMARK 465 GLY 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 465 HIS B 137 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO B 100 CA - N - CD ANGL. DEV. = -14.7 DEGREES 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 ASP A 68 84.54 -157.67 REMARK 500 ASN A 70 31.09 -95.43 REMARK 500 ASN A 104 57.61 -94.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-42381 RELATED DB: EMDB REMARK 900 T33-ML35 - DESIGNED TETRAHEDRAL PROTEIN CAGE USING MACHINE LEARNING REMARK 900 ALGORITHMS DBREF 8UMP A 1 122 PDB 8UMP 8UMP 1 122 DBREF 8UMP B 11 137 PDB 8UMP 8UMP 11 137 SEQRES 1 A 122 MET ASN LEU ALA GLU LYS MET TYR LYS ALA GLY GLN ILE SEQRES 2 A 122 GLU PHE ALA LYS GLY ASN TYR GLU THR ALA ILE ILE ALA SEQRES 3 A 122 TYR THR LEU ALA LEU LEU LYS ASP PRO ASN ASN ALA GLU SEQRES 4 A 122 ALA TRP TYR ASN LEU GLY GLU ALA TYR LEU ALA LEU GLY SEQRES 5 A 122 ASN TYR GLU GLU ALA ILE GLU ALA TYR GLN LYS ALA LEU SEQRES 6 A 122 GLU LEU ASP PRO ASN ASN ALA GLU ALA TRP TYR ASN LEU SEQRES 7 A 122 GLY GLU ALA TYR LEU ALA LEU GLY ASP TYR ASP ASN ALA SEQRES 8 A 122 ILE GLU ALA PHE THR LYS ALA LEU GLU LEU ASP PRO ASN SEQRES 9 A 122 ASN LYS THR ALA LYS ALA GLY LEU LYS LEU ALA LYS GLU SEQRES 10 A 122 LYS LYS ALA LEU GLU SEQRES 1 B 127 MET THR ASP LEU SER SER LEU ILE GLU THR ALA ASP LEU SEQRES 2 B 127 ARG LEU LEU LEU THR THR VAL PRO THR GLU THR GLU ALA SEQRES 3 B 127 LEU TYR LEU ALA LEU ALA ALA VAL GLU LYS GLY LEU ALA SEQRES 4 B 127 ALA GLU VAL LEU ILE THR PRO VAL THR ARG VAL ARG ARG SEQRES 5 B 127 GLU ASN GLY LYS LEU VAL VAL GLU ASP VAL TYR ARG LEU SEQRES 6 B 127 SER PHE LYS THR THR ARG GLU ARG LEU ASP ALA LEU VAL SEQRES 7 B 127 ALA TRP LEU GLN ARG ARG HIS PRO LEU ALA LEU PRO GLU SEQRES 8 B 127 CYS LEU VAL LEU THR PRO ILE ALA SER SER VAL ALA TYR SEQRES 9 B 127 ARG ASP TRP LEU ARG SER SER LEU GLN GLY GLY SER HIS SEQRES 10 B 127 HIS TRP GLY GLY HIS HIS HIS HIS HIS HIS HELIX 1 AA1 ASN A 2 LYS A 17 1 16 HELIX 2 AA2 ASN A 19 ASP A 34 1 16 HELIX 3 AA3 ASN A 37 GLY A 52 1 16 HELIX 4 AA4 ASN A 53 ASP A 68 1 16 HELIX 5 AA5 ASN A 71 LEU A 85 1 15 HELIX 6 AA6 ASP A 87 ASP A 102 1 16 HELIX 7 AA7 ASN A 105 LEU A 121 1 17 HELIX 8 AA8 THR B 32 LYS B 46 1 15 HELIX 9 AA9 ARG B 83 HIS B 95 1 13 HELIX 10 AB1 VAL B 112 SER B 121 1 10 SHEET 1 AA1 2 LEU B 17 GLU B 19 0 SHEET 2 AA1 2 ALA B 109 SER B 111 -1 O SER B 110 N ILE B 18 SHEET 1 AA2 4 GLU B 51 GLU B 63 0 SHEET 2 AA2 4 LYS B 66 THR B 80 -1 O ARG B 74 N THR B 55 SHEET 3 AA2 4 LEU B 23 VAL B 30 -1 N THR B 28 O LEU B 75 SHEET 4 AA2 4 LEU B 103 LEU B 105 -1 O LEU B 103 N LEU B 27 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