HEADER DE NOVO PROTEIN 06-FEB-23 8I8Y TITLE A MUTANT OF THE C-TERMINAL COMPLEX OF PROTEINS 4.1G AND NUMA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENGINEERED PROTEIN; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ENGINEERED PROTEIN; COMPND 7 CHAIN: A; 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; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 8 ORGANISM_TAXID: 32630; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS A COMPUTATIONAL DESIGN MUTANT OF A FUSION PROTEIN FROM THE C TERMINAL KEYWDS 2 OF 4.1G AND NUMA, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.HU REVDAT 3 15-NOV-23 8I8Y 1 REMARK REVDAT 2 04-OCT-23 8I8Y 1 JRNL REVDAT 1 19-APR-23 8I8Y 0 JRNL AUTH X.HU,Y.XU,C.WANG,Y.LIU,L.ZHANG,J.ZHANG,W.WANG,Q.CHEN,H.LIU JRNL TITL COMBINED PREDICTION AND DESIGN REVEALS THE TARGET JRNL TITL 2 RECOGNITION MECHANISM OF AN INTRINSICALLY DISORDERED PROTEIN JRNL TITL 3 INTERACTION DOMAIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 03120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 37722056 JRNL DOI 10.1073/PNAS.2305603120 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 3 NUMBER OF REFLECTIONS : 5418 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.284 REMARK 3 R VALUE (WORKING SET) : 0.281 REMARK 3 FREE R VALUE : 0.340 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 258 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 47.7200 - 3.6500 0.94 2658 126 0.2624 0.3151 REMARK 3 2 3.6500 - 2.9000 0.94 2502 132 0.3607 0.4287 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) : 0.362 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.169 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 97.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 93.15 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 : 0.003 1094 REMARK 3 ANGLE : 0.604 1482 REMARK 3 CHIRALITY : 0.059 182 REMARK 3 PLANARITY : 0.003 194 REMARK 3 DIHEDRAL : 12.281 408 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 8I8Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300033432. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-SEP-22 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 : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5420 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 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 (%) : 93.7 REMARK 200 DATA REDUNDANCY : 20.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.3600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: SAD REMARK 200 SOFTWARE USED: CRANK2 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 90% (0.2 M TRIMETHYLAMINE N-OXIDE REMARK 280 DIHYDRATE, 0.1 M TRIS, PH 9.4, 20% W/V POLYETHYLENE GLYCOL REMARK 280 MONOMETHYL ETHER 2,000) AND 10% 0.1 M TCEP HYDROCHLORIDE, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 46.58550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 46.58550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 27.78100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 46.58550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 46.58550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.78100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 46.58550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.58550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 27.78100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 46.58550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.58550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.78100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 ASP B 17 CG OD1 OD2 REMARK 470 MSE B 42 CG SE CE REMARK 470 GLU B 57 CG CD OE1 OE2 REMARK 470 GLU B 58 CG CD OE1 OE2 REMARK 470 GLU B 60 CG CD OE1 OE2 REMARK 470 MSE B 71 CG SE CE REMARK 470 GLU A 11 CG CD OE1 OE2 REMARK 470 ASP A 21 CG OD1 OD2 REMARK 470 MSE A 42 CG SE CE REMARK 470 GLU A 57 CG CD OE1 OE2 REMARK 470 GLU A 60 CG CD OE1 OE2 REMARK 470 ASN A 68 CG OD1 ND2 REMARK 470 MSE A 71 CG SE CE 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 76 112.28 -160.36 REMARK 500 REMARK 500 REMARK: NULL DBREF 8I8Y B 9 78 PDB 8I8Y 8I8Y 9 78 DBREF 8I8Y A 8 78 PDB 8I8Y 8I8Y 8 78 SEQRES 1 B 70 VAL ILE GLU LYS ARG ILE VAL ILE ASP GLY ASP GLY ASP SEQRES 2 B 70 ILE ASP HIS ASP GLN ALA LEU ALA GLN ALA ILE ARG GLU SEQRES 3 B 70 ALA ARG GLU GLN HIS PRO ASP MSE SER VAL THR ARG VAL SEQRES 4 B 70 VAL VAL ASN LYS GLU THR GLU LEU ALA GLU GLU GLY GLU SEQRES 5 B 70 ASP ARG THR ARG GLN ILE ILE ASN ILE THR MSE THR LYS SEQRES 6 B 70 LYS LEU ASP VAL TRP SEQRES 1 A 71 THR VAL ILE GLU LYS ARG ILE VAL ILE ASP GLY ASP GLY SEQRES 2 A 71 ASP ILE ASP HIS ASP GLN ALA LEU ALA GLN ALA ILE ARG SEQRES 3 A 71 GLU ALA ARG GLU GLN HIS PRO ASP MSE SER VAL THR ARG SEQRES 4 A 71 VAL VAL VAL ASN LYS GLU THR GLU LEU ALA GLU GLU GLY SEQRES 5 A 71 GLU ASP ARG THR ARG GLN ILE ILE ASN ILE THR MSE THR SEQRES 6 A 71 LYS LYS LEU ASP VAL TRP HET MSE B 42 5 HET MSE B 71 5 HET MSE A 42 5 HET MSE A 71 5 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) HELIX 1 AA1 ASP B 23 HIS B 39 1 17 HELIX 2 AA2 ASP A 23 HIS A 39 1 17 SHEET 1 AA1 6 ILE B 10 ASP B 17 0 SHEET 2 AA1 6 ARG B 62 LYS B 73 -1 O ILE B 67 N ILE B 14 SHEET 3 AA1 6 MSE B 42 GLU B 54 -1 N THR B 45 O THR B 70 SHEET 4 AA1 6 MSE A 42 GLU A 54 -1 O VAL A 49 N THR B 53 SHEET 5 AA1 6 THR A 63 LYS A 73 -1 O THR A 70 N THR A 45 SHEET 6 AA1 6 VAL A 9 ILE A 16 -1 N LYS A 12 O ILE A 69 LINK C ASP B 41 N MSE B 42 1555 1555 1.33 LINK C MSE B 42 N SER B 43 1555 1555 1.33 LINK C THR B 70 N MSE B 71 1555 1555 1.34 LINK C MSE B 71 N THR B 72 1555 1555 1.33 LINK C ASP A 41 N MSE A 42 1555 1555 1.34 LINK C MSE A 42 N SER A 43 1555 1555 1.33 LINK C THR A 70 N MSE A 71 1555 1555 1.34 LINK C MSE A 71 N THR A 72 1555 1555 1.33 CRYST1 93.171 93.171 55.562 90.00 90.00 90.00 P 42 21 2 8 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 0.010733 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010733 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017998 0.00000