HEADER DE NOVO PROTEIN 05-MAY-23 8OYV TITLE DE NOVO DESIGNED CLAUDIN FOLD CLF_4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DE NOVO DESIGNED SOLUBLE CLAUDIN; 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 CLAUDIN, SOLUBILIZED, DE NOVO DESIGNED, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.PACESA,B.E.CORREIA REVDAT 3 14-AUG-24 8OYV 1 JRNL REVDAT 2 27-MAR-24 8OYV 1 JRNL REVDAT 1 18-OCT-23 8OYV 0 JRNL AUTH C.A.GOVERDE,M.PACESA,N.GOLDBACH,L.J.DORNFELD,P.E.M.BALBI, JRNL AUTH 2 S.GEORGEON,S.ROSSET,S.KAPOOR,J.CHOUDHURY,J.DAUPARAS, JRNL AUTH 3 C.SCHELLHAAS,S.KOZLOV,D.BAKER,S.OVCHINNIKOV,A.J.VECCHIO, JRNL AUTH 4 B.E.CORREIA JRNL TITL COMPUTATIONAL DESIGN OF SOLUBLE AND FUNCTIONAL MEMBRANE JRNL TITL 2 PROTEIN ANALOGUES. JRNL REF NATURE V. 631 449 2024 JRNL REFN ESSN 1476-4687 JRNL PMID 38898281 JRNL DOI 10.1038/S41586-024-07601-Y REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.A.GOVERDE,M.PACESA,N.GOLDBACH,L.J.DORNFELD,P.E.M.BALBI, REMARK 1 AUTH 2 S.GEORGEON,S.ROSSET,S.KAPOOR,J.CHOUDHURY,J.DAUPARAS, REMARK 1 AUTH 3 C.SCHELLHAAS,S.KOZLOV,D.BAKER,S.OVCHINNIKOV,A.J.VECCHIO, REMARK 1 AUTH 4 B.E.CORREIA REMARK 1 TITL COMPUTATIONAL DESIGN OF SOLUBLE FUNCTIONAL ANALOGUES OF REMARK 1 TITL 2 INTEGRAL MEMBRANE PROTEINS. REMARK 1 REF BIORXIV 2024 REMARK 1 REFN ISSN 2692-8205 REMARK 1 PMID 38496615 REMARK 1 DOI 10.1101/2023.05.09.540044 REMARK 2 REMARK 2 RESOLUTION. 2.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 3 NUMBER OF REFLECTIONS : 7981 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.274 REMARK 3 R VALUE (WORKING SET) : 0.273 REMARK 3 FREE R VALUE : 0.318 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 367 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 52.3500 - 4.0300 0.93 2718 119 0.2310 0.2611 REMARK 3 2 4.0300 - 3.2000 0.75 2158 95 0.3290 0.4034 REMARK 3 3 3.2000 - 2.7900 0.96 2738 153 0.3966 0.4428 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.458 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 42.910 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 77.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 97.64 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 2978 REMARK 3 ANGLE : 0.477 3992 REMARK 3 CHIRALITY : 0.036 460 REMARK 3 PLANARITY : 0.004 508 REMARK 3 DIHEDRAL : 13.332 1206 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 : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 2 through 101 or REMARK 3 resid 108 through 186)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : chain "B" REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8OYV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1292130309. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8007 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.790 REMARK 200 RESOLUTION RANGE LOW (A) : 52.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 200 DATA REDUNDANCY : 2.500 REMARK 200 R MERGE (I) : 0.10690 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 1.58800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.420 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 (%): 40.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE PH 5, 0.1 M REMARK 280 SODIUM/POTASSIUM PHOSPHATE PH 5.5, 0.1M RUBIDIUM CHLORIDE, 25% V/ REMARK 280 V PEG SMEAR MEDIUM, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 0 REMARK 465 GLU A 102 REMARK 465 GLU A 103 REMARK 465 ASP A 104 REMARK 465 GLY A 105 REMARK 465 GLU A 106 REMARK 465 GLY A 188 REMARK 465 HIS A 189 REMARK 465 HIS A 190 REMARK 465 HIS A 191 REMARK 465 HIS A 192 REMARK 465 HIS A 193 REMARK 465 HIS A 194 REMARK 465 MET B 0 REMARK 465 ASN B 1 REMARK 465 GLU B 102 REMARK 465 GLU B 103 REMARK 465 ASP B 104 REMARK 465 GLY B 105 REMARK 465 GLU B 106 REMARK 465 LEU B 107 REMARK 465 SER B 187 REMARK 465 GLY B 188 REMARK 465 HIS B 189 REMARK 465 HIS B 190 REMARK 465 HIS B 191 REMARK 465 HIS B 192 REMARK 465 HIS B 193 REMARK 465 HIS B 194 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 34 99.50 -62.88 REMARK 500 LYS A 147 33.92 -72.66 REMARK 500 TYR A 158 23.71 -76.89 REMARK 500 LYS B 147 33.57 -72.98 REMARK 500 TYR B 158 22.00 -78.24 REMARK 500 REMARK 500 REMARK: NULL DBREF 8OYV A 0 194 PDB 8OYV 8OYV 0 194 DBREF 8OYV B 0 194 PDB 8OYV 8OYV 0 194 SEQRES 1 A 195 MET ASN GLU GLU LYS ARG GLU GLU LEU LEU GLU GLU ALA SEQRES 2 A 195 LYS ARG LEU LEU GLU GLU SER LEU LYS LEU LEU LYS GLN SEQRES 3 A 195 ALA TYR ASN THR PRO ILE GLU ILE ASP LEU PRO ILE SER SEQRES 4 A 195 GLY GLY VAL LYS ALA ILE LEU TYR ASN GLY LYS VAL TYR SEQRES 5 A 195 LEU ILE TYR GLU ASN GLY LYS VAL GLU GLU ILE GLU ILE SEQRES 6 A 195 PRO GLU ASP ASP ILE LEU TYR PRO ILE TYR ASN LYS TYR SEQRES 7 A 195 ILE GLU THR LEU LYS GLU ALA LEU LYS THR VAL GLU LYS SEQRES 8 A 195 LEU GLN GLU GLU LEU GLU GLU LEU LEU GLU ASN GLU GLU SEQRES 9 A 195 ASP GLY GLU LEU SER GLU GLU GLU ARG LEU GLU LYS LEU SEQRES 10 A 195 LYS GLU LEU ALA GLU GLU LEU LYS GLU THR ALA GLU LYS SEQRES 11 A 195 LEU LEU LYS SER ILE GLU GLU PHE SER LYS PHE LEU GLU SEQRES 12 A 195 GLU LEU LYS LYS LYS LEU PRO LYS ASN ILE LYS LEU ASN SEQRES 13 A 195 ILE ASN TYR SER SER ILE ASN LEU ALA LYS GLU ALA ALA SEQRES 14 A 195 GLU LYS ALA LEU GLU ALA SER GLU LEU LEU GLU GLU VAL SEQRES 15 A 195 TYR GLU SER SER GLY SER GLY HIS HIS HIS HIS HIS HIS SEQRES 1 B 195 MET ASN GLU GLU LYS ARG GLU GLU LEU LEU GLU GLU ALA SEQRES 2 B 195 LYS ARG LEU LEU GLU GLU SER LEU LYS LEU LEU LYS GLN SEQRES 3 B 195 ALA TYR ASN THR PRO ILE GLU ILE ASP LEU PRO ILE SER SEQRES 4 B 195 GLY GLY VAL LYS ALA ILE LEU TYR ASN GLY LYS VAL TYR SEQRES 5 B 195 LEU ILE TYR GLU ASN GLY LYS VAL GLU GLU ILE GLU ILE SEQRES 6 B 195 PRO GLU ASP ASP ILE LEU TYR PRO ILE TYR ASN LYS TYR SEQRES 7 B 195 ILE GLU THR LEU LYS GLU ALA LEU LYS THR VAL GLU LYS SEQRES 8 B 195 LEU GLN GLU GLU LEU GLU GLU LEU LEU GLU ASN GLU GLU SEQRES 9 B 195 ASP GLY GLU LEU SER GLU GLU GLU ARG LEU GLU LYS LEU SEQRES 10 B 195 LYS GLU LEU ALA GLU GLU LEU LYS GLU THR ALA GLU LYS SEQRES 11 B 195 LEU LEU LYS SER ILE GLU GLU PHE SER LYS PHE LEU GLU SEQRES 12 B 195 GLU LEU LYS LYS LYS LEU PRO LYS ASN ILE LYS LEU ASN SEQRES 13 B 195 ILE ASN TYR SER SER ILE ASN LEU ALA LYS GLU ALA ALA SEQRES 14 B 195 GLU LYS ALA LEU GLU ALA SER GLU LEU LEU GLU GLU VAL SEQRES 15 B 195 TYR GLU SER SER GLY SER GLY HIS HIS HIS HIS HIS HIS FORMUL 3 HOH *(H2 O) HELIX 1 AA1 ASN A 1 THR A 29 1 29 HELIX 2 AA2 ILE A 69 ASN A 101 1 33 HELIX 3 AA3 SER A 108 LYS A 147 1 40 HELIX 4 AA4 TYR A 158 SER A 187 1 30 HELIX 5 AA5 GLU B 3 THR B 29 1 27 HELIX 6 AA6 ILE B 69 ASN B 101 1 33 HELIX 7 AA7 GLU B 109 LYS B 147 1 39 HELIX 8 AA8 TYR B 158 SER B 185 1 28 SHEET 1 AA1 4 ILE A 31 ASP A 34 0 SHEET 2 AA1 4 LYS A 42 TYR A 46 -1 O ALA A 43 N ILE A 33 SHEET 3 AA1 4 LYS A 49 ILE A 53 -1 O TYR A 51 N ILE A 44 SHEET 4 AA1 4 VAL A 59 ILE A 62 -1 O GLU A 60 N LEU A 52 SHEET 1 AA2 4 ILE B 31 ASP B 34 0 SHEET 2 AA2 4 LYS B 42 TYR B 46 -1 O ALA B 43 N ILE B 33 SHEET 3 AA2 4 LYS B 49 ILE B 53 -1 O TYR B 51 N ILE B 44 SHEET 4 AA2 4 VAL B 59 ILE B 62 -1 O GLU B 60 N LEU B 52 CRYST1 35.560 50.770 54.930 107.61 90.49 90.06 P 1 2 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 0.028121 0.000029 0.000262 0.00000 SCALE2 0.000000 0.019697 0.006252 0.00000 SCALE3 0.000000 0.000000 0.019101 0.00000 MTRIX1 1 0.999967 0.000296 0.008139 -17.68149 1 MTRIX2 1 0.000318 -0.999996 -0.002684 -3.03858 1 MTRIX3 1 0.008139 0.002687 -0.999963 28.77607 1