HEADER DE NOVO PROTEIN 11-MAR-21 7M0Q TITLE CRYSTAL STRUCTURE OF DEEP NETWORK HALLUCINATED PROTEIN 0738_MOD COMPND MOL_ID: 1; COMPND 2 MOLECULE: NETWORK HALLUCINATED PROTEIN 0738_MOD; COMPND 3 CHAIN: A, B; 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 ALPHA-BETA FOLD, MACHINE LEARNING, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.J.PELLOCK,A.K.BERA,I.ANISHCHENKO,D.BAKER REVDAT 2 03-APR-24 7M0Q 1 REMARK REVDAT 1 29-DEC-21 7M0Q 0 JRNL AUTH I.ANISHCHENKO,S.J.PELLOCK,T.M.CHIDYAUSIKU,T.A.RAMELOT, JRNL AUTH 2 S.OVCHINNIKOV,J.HAO,K.BAFNA,C.NORN,A.KANG,A.K.BERA,F.DIMAIO, JRNL AUTH 3 L.CARTER,C.M.CHOW,G.T.MONTELIONE,D.BAKER JRNL TITL DE NOVO PROTEIN DESIGN BY DEEP NETWORK HALLUCINATION. JRNL REF NATURE V. 600 547 2021 JRNL REFN ESSN 1476-4687 JRNL PMID 34853475 JRNL DOI 10.1038/S41586-021-04184-W REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.1_4122 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 7132 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 363 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 3.4600 - 2.4900 1.00 2434 132 0.2388 0.2479 REMARK 3 2 2.4900 - 2.4000 0.77 1892 92 0.2902 0.3129 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) : 0.199 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.24 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 : 0.002 1499 REMARK 3 ANGLE : 0.430 2029 REMARK 3 CHIRALITY : 0.040 236 REMARK 3 PLANARITY : 0.004 262 REMARK 3 DIHEDRAL : 12.218 544 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 7M0Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255433. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7742 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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: COMPUTATIONAL MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION: 3.7 MG/ML REMARK 280 SAMPLE BUFFER:20 MM HEPES, 50 MM NACL, PH 7.4 CRYSTALLANTS: 40% REMARK 280 V/V PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), 15% V/V ETHANOL, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.49733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 54.99467 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: 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 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 -16 REMARK 465 GLY A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 SER A -6 REMARK 465 SER A -5 REMARK 465 GLY A -4 REMARK 465 LEU A -3 REMARK 465 VAL A -2 REMARK 465 PRO A -1 REMARK 465 ARG A 0 REMARK 465 GLY A 1 REMARK 465 GLU A 13 REMARK 465 ASP A 14 REMARK 465 PRO A 15 REMARK 465 LYS A 16 REMARK 465 LYS A 17 REMARK 465 GLY A 18 REMARK 465 LYS A 19 REMARK 465 MET B -16 REMARK 465 GLY B -15 REMARK 465 SER B -14 REMARK 465 SER B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 SER B -6 REMARK 465 SER B -5 REMARK 465 GLY B -4 REMARK 465 LEU B -3 REMARK 465 VAL B -2 REMARK 465 PRO B -1 REMARK 465 ARG B 0 REMARK 465 GLY B 1 REMARK 465 SER B 2 REMARK 465 HIS B 3 REMARK 465 PRO B 15 REMARK 465 LYS B 16 REMARK 465 LYS B 17 REMARK 465 GLY B 18 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 LEU A 47 CG CD1 CD2 REMARK 470 GLN A 48 CG CD OE1 NE2 REMARK 470 ASP A 49 CG OD1 OD2 REMARK 470 GLU A 50 CG CD OE1 OE2 REMARK 470 TRP A 52 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 52 CZ3 CH2 REMARK 470 ASP A 53 CG OD1 OD2 REMARK 470 GLU B 50 CG CD OE1 OE2 REMARK 470 ASP B 53 CG OD1 OD2 REMARK 470 PHE B 65 CG CD1 CD2 CE1 CE2 CZ 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 GLN A 48 -160.40 -77.84 REMARK 500 ASP A 49 -110.94 56.02 REMARK 500 TRP A 52 -66.60 -152.90 REMARK 500 ASP B 53 -96.26 -93.86 REMARK 500 REMARK 500 REMARK: NULL DBREF 7M0Q A -16 104 PDB 7M0Q 7M0Q -16 104 DBREF 7M0Q B -16 104 PDB 7M0Q 7M0Q -16 104 SEQRES 1 A 121 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 121 LEU VAL PRO ARG GLY SER HIS MET ASN ILE GLN VAL SER SEQRES 3 A 121 LEU GLN TRP GLU ASP PRO LYS LYS GLY LYS VAL PHE SER SEQRES 4 A 121 HIS THR VAL ASN ILE PRO PRO GLY GLY THR ALA GLU GLN SEQRES 5 A 121 ILE ALA ASP ASN ILE LEU ASP MET ALA ARG SER LEU GLN SEQRES 6 A 121 ASP GLU GLY TRP ASP LYS LEU THR VAL GLN VAL THR VAL SEQRES 7 A 121 ASN PRO GLY PHE PRO LYS GLU THR ALA MET ARG VAL ALA SEQRES 8 A 121 ALA ALA LEU LYS GLU ALA PHE GLU ASP ARG GLY LEU ARG SEQRES 9 A 121 LEU THR SER ILE GLU THR SER GLY ASN SER ILE HIS LEU SEQRES 10 A 121 LYS PHE ARG TYR SEQRES 1 B 121 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 121 LEU VAL PRO ARG GLY SER HIS MET ASN ILE GLN VAL SER SEQRES 3 B 121 LEU GLN TRP GLU ASP PRO LYS LYS GLY LYS VAL PHE SER SEQRES 4 B 121 HIS THR VAL ASN ILE PRO PRO GLY GLY THR ALA GLU GLN SEQRES 5 B 121 ILE ALA ASP ASN ILE LEU ASP MET ALA ARG SER LEU GLN SEQRES 6 B 121 ASP GLU GLY TRP ASP LYS LEU THR VAL GLN VAL THR VAL SEQRES 7 B 121 ASN PRO GLY PHE PRO LYS GLU THR ALA MET ARG VAL ALA SEQRES 8 B 121 ALA ALA LEU LYS GLU ALA PHE GLU ASP ARG GLY LEU ARG SEQRES 9 B 121 LEU THR SER ILE GLU THR SER GLY ASN SER ILE HIS LEU SEQRES 10 B 121 LYS PHE ARG TYR FORMUL 3 HOH *19(H2 O) HELIX 1 AA1 THR A 32 ARG A 45 1 14 HELIX 2 AA2 SER A 46 GLN A 48 5 3 HELIX 3 AA3 PRO A 66 ASP A 83 1 18 HELIX 4 AA4 THR B 32 GLU B 50 1 19 HELIX 5 AA5 PRO B 66 ASP B 83 1 18 SHEET 1 AA110 SER A 22 ILE A 27 0 SHEET 2 AA110 ASN A 5 GLN A 11 -1 N LEU A 10 O HIS A 23 SHEET 3 AA110 THR A 56 ASN A 62 -1 O ASN A 62 N ASN A 5 SHEET 4 AA110 ILE A 98 ARG A 103 -1 O PHE A 102 N VAL A 57 SHEET 5 AA110 ARG A 87 GLU A 92 -1 N GLU A 92 O HIS A 99 SHEET 6 AA110 ARG B 87 SER B 94 -1 O THR B 93 N THR A 89 SHEET 7 AA110 SER B 97 ARG B 103 -1 O HIS B 99 N GLU B 92 SHEET 8 AA110 LEU B 55 VAL B 61 -1 N VAL B 57 O PHE B 102 SHEET 9 AA110 ILE B 6 TRP B 12 -1 N SER B 9 O GLN B 58 SHEET 10 AA110 PHE B 21 ILE B 27 -1 O PHE B 21 N TRP B 12 CISPEP 1 ASN A 62 PRO A 63 0 -1.83 CISPEP 2 PHE A 65 PRO A 66 0 -2.12 CRYST1 46.291 46.291 82.492 90.00 90.00 120.00 P 31 6 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 0.021602 0.012472 0.000000 0.00000 SCALE2 0.000000 0.024944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012122 0.00000