HEADER DE NOVO PROTEIN 03-DEC-20 7DMF TITLE A DE NOVO PROTEIN THAT RIGIDLY EXTENDS THE STRUCTURE OF TVHS-LIKE TITLE 2 DOMAIN IN TEPSIN WITH A NEW DESIGNED DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED PROTEIN EXTD-3; 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 K-12; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS ALL HELIX, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.XU REVDAT 6 29-NOV-23 7DMF 1 REMARK REVDAT 5 09-MAR-22 7DMF 1 REMARK REVDAT 4 02-MAR-22 7DMF 1 JRNL REVDAT 3 23-FEB-22 7DMF 1 COMPND JRNL REVDAT 2 16-FEB-22 7DMF 1 AUTHOR JRNL REVDAT 1 08-DEC-21 7DMF 0 JRNL AUTH B.HUANG,Y.XU,X.HU,Y.LIU,S.LIAO,J.ZHANG,C.HUANG,J.HONG, JRNL AUTH 2 Q.CHEN,H.LIU JRNL TITL A BACKBONE-CENTRED ENERGY FUNCTION OF NEURAL NETWORKS FOR JRNL TITL 2 PROTEIN DESIGN. JRNL REF NATURE V. 602 523 2022 JRNL REFN ESSN 1476-4687 JRNL PMID 35140398 JRNL DOI 10.1038/S41586-021-04383-5 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.3 REMARK 3 NUMBER OF REFLECTIONS : 8396 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.232 REMARK 3 FREE R VALUE : 0.269 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.800 REMARK 3 FREE R VALUE TEST SET COUNT : 823 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 26.1810 - 3.9951 0.84 1399 195 0.2118 0.2348 REMARK 3 2 3.9951 - 3.1728 0.90 1530 140 0.2429 0.3046 REMARK 3 3 3.1728 - 2.7722 0.78 1293 150 0.2443 0.2637 REMARK 3 4 2.7722 - 2.5190 0.70 1178 115 0.2350 0.2754 REMARK 3 5 2.5190 - 2.3385 0.66 1092 126 0.2403 0.3286 REMARK 3 6 2.3385 - 2.2010 0.64 1081 97 0.2398 0.2986 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.70 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 : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 6 THROUGH 194) REMARK 3 ORIGIN FOR THE GROUP (A): 14.4114 -25.9500 3.0185 REMARK 3 T TENSOR REMARK 3 T11: 0.2657 T22: 0.2198 REMARK 3 T33: 0.2218 T12: -0.0332 REMARK 3 T13: 0.0082 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.8771 L22: 0.6128 REMARK 3 L33: 0.8363 L12: -0.4956 REMARK 3 L13: 0.6413 L23: -0.3737 REMARK 3 S TENSOR REMARK 3 S11: 0.1169 S12: -0.0478 S13: -0.1763 REMARK 3 S21: 0.0396 S22: -0.0374 S23: -0.0162 REMARK 3 S31: 0.0968 S32: 0.0691 S33: -0.0864 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 7DMF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1300019705. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-OCT-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97892 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11185 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 19.60 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 17.20 REMARK 200 R MERGE FOR SHELL (I) : 0.56600 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: NULL REMARK 200 STARTING MODEL: 5WF2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V POLYETHYLENE GLYCOL 3350, PH REMARK 280 7.0, 0.2M POTASSIUM CHLORIDE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 52.86067 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 26.43033 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 39.64550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 13.21517 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 66.07583 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 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 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 LEU A 40 -163.77 -116.65 REMARK 500 LEU A 94 -163.30 -78.99 REMARK 500 ASP A 95 39.29 -166.24 REMARK 500 TYR A 98 16.30 81.08 REMARK 500 REMARK 500 REMARK: NULL DBREF 7DMF A 6 194 PDB 7DMF 7DMF 6 194 SEQRES 1 A 189 ASP CYS GLN GLN GLU LEU SER LEU VAL GLN THR VAL THR SEQRES 2 A 189 ARG GLY SER ARG ALA PHE LEU SER ARG GLU GLU ALA GLN SEQRES 3 A 189 HIS PHE VAL LYS GLU CYS GLY LEU LEU ASN CYS GLU ALA SEQRES 4 A 189 VAL LEU GLU LEU LEU ILE CYS HIS LEU ARG LEU GLY MET SEQRES 5 A 189 GLU ILE MET LYS LEU GLY ARG GLN LEU ARG GLU ALA VAL SEQRES 6 A 189 ARG ALA ASN ASP VAL ASP ALA MET LEU LYS ILE ALA LYS SEQRES 7 A 189 GLU ILE ILE LYS VAL ILE GLY GLU THR GLY LEU ASP GLU SEQRES 8 A 189 VAL TYR ARG GLN LEU LEU LYS ALA ALA LYS GLU PHE LEU SEQRES 9 A 189 GLU ARG ARG ALA GLU ASN PHE SER HIS GLU GLU ALA VAL SEQRES 10 A 189 ALA PHE ALA GLN GLN ILE ILE GLN LEU ILE LYS GLN VAL SEQRES 11 A 189 GLU CYS VAL GLN MET ARG ALA LEU GLY ALA VAL ALA SER SEQRES 12 A 189 LEU GLY CYS THR ASP LEU LEU PRO GLN GLU HIS ILE LEU SEQRES 13 A 189 LEU LEU THR ARG PRO ARG LEU GLN GLU LEU SER ALA GLY SEQRES 14 A 189 SER PRO GLY PRO VAL THR ASN LYS ALA THR LYS ILE LEU SEQRES 15 A 189 ARG HIS PHE GLU ALA SER CYS FORMUL 2 HOH *5(H2 O) HELIX 1 AA1 ASP A 6 THR A 18 1 13 HELIX 2 AA2 SER A 26 LEU A 40 1 15 HELIX 3 AA3 ASN A 41 ASN A 73 1 33 HELIX 4 AA4 ASP A 74 THR A 92 1 19 HELIX 5 AA5 TYR A 98 ARG A 111 1 14 HELIX 6 AA6 ARG A 112 GLU A 114 5 3 HELIX 7 AA7 SER A 117 CYS A 151 1 35 HELIX 8 AA8 PRO A 156 ALA A 173 1 18 HELIX 9 AA9 GLY A 177 CYS A 194 1 18 CRYST1 69.727 69.727 79.291 90.00 90.00 120.00 P 65 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 0.014342 0.008280 0.000000 0.00000 SCALE2 0.000000 0.016560 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012612 0.00000