HEADER DE NOVO PROTEIN 20-MAR-22 7UDK TITLE CRYSTAL STRUCTURE OF DESIGNED HELICAL REPEAT PROTEIN RPB_LRP2_R4 BOUND TITLE 2 TO LRPX4 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DESIGNED HELICAL REPEAT PROTEIN (DHR) RPB_LRP2_R4; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 4XLRP; 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 B; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 37762; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630 KEYWDS PEPTIDE BINDING, DESIGNED HELICAL REPEAT (DHR), DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.CHANG,R.L.REDLER,G.BHABHA,D.C.EKIERT REVDAT 4 03-APR-24 7UDK 1 REMARK REVDAT 3 03-MAY-23 7UDK 1 JRNL REVDAT 2 19-APR-23 7UDK 1 JRNL REVDAT 1 22-MAR-23 7UDK 0 JRNL AUTH K.WU,H.BAI,Y.T.CHANG,R.REDLER,K.E.MCNALLY,W.SHEFFLER, JRNL AUTH 2 T.J.BRUNETTE,D.R.HICKS,T.E.MORGAN,T.J.STEVENS,A.BROERMAN, JRNL AUTH 3 I.GORESHNIK,M.DEWITT,C.M.CHOW,Y.SHEN,L.STEWART,E.DERIVERY, JRNL AUTH 4 D.A.SILVA,G.BHABHA,D.C.EKIERT,D.BAKER JRNL TITL DE NOVO DESIGN OF MODULAR PEPTIDE-BINDING PROTEINS BY JRNL TITL 2 SUPERHELICAL MATCHING. JRNL REF NATURE V. 616 581 2023 JRNL REFN ESSN 1476-4687 JRNL PMID 37020023 JRNL DOI 10.1038/S41586-023-05909-9 REMARK 2 REMARK 2 RESOLUTION. 3.18 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) : 3.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.1 REMARK 3 NUMBER OF REFLECTIONS : 5904 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 294 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 35.3900 - 4.0100 0.99 3192 168 0.1845 0.2375 REMARK 3 2 4.0100 - 3.1800 0.79 2418 126 0.3311 0.3515 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) : 0.225 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.248 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 132.6 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 161.9 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 : 0.004 1490 REMARK 3 ANGLE : 0.616 1998 REMARK 3 CHIRALITY : 0.042 228 REMARK 3 PLANARITY : 0.006 266 REMARK 3 DIHEDRAL : 3.786 198 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 86 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.9005 0.8523 -30.0351 REMARK 3 T TENSOR REMARK 3 T11: 1.6553 T22: 1.0735 REMARK 3 T33: 1.0833 T12: 0.3985 REMARK 3 T13: -0.0134 T23: 0.0708 REMARK 3 L TENSOR REMARK 3 L11: 5.6412 L22: 7.4283 REMARK 3 L33: 5.0391 L12: 0.4476 REMARK 3 L13: 0.8946 L23: -1.3519 REMARK 3 S TENSOR REMARK 3 S11: 0.4731 S12: -0.3661 S13: -0.1423 REMARK 3 S21: 0.0892 S22: -0.0857 S23: -0.4826 REMARK 3 S31: -0.2383 S32: 0.1570 S33: -0.3929 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 87 THROUGH 105 ) REMARK 3 ORIGIN FOR THE GROUP (A): -37.4048 12.0808 -23.6163 REMARK 3 T TENSOR REMARK 3 T11: 2.4650 T22: 0.8439 REMARK 3 T33: 1.2621 T12: 0.8956 REMARK 3 T13: 0.2890 T23: -0.2391 REMARK 3 L TENSOR REMARK 3 L11: 5.5800 L22: 2.7665 REMARK 3 L33: 6.6388 L12: 1.2134 REMARK 3 L13: 0.2762 L23: -3.0900 REMARK 3 S TENSOR REMARK 3 S11: -0.8452 S12: 0.0267 S13: 0.8274 REMARK 3 S21: 0.1252 S22: 0.7842 S23: 0.3866 REMARK 3 S31: 0.1287 S32: -1.5574 S33: -0.2095 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 106 THROUGH 171 ) REMARK 3 ORIGIN FOR THE GROUP (A): -36.2025 20.9205 -17.0313 REMARK 3 T TENSOR REMARK 3 T11: 1.2602 T22: 1.0702 REMARK 3 T33: 1.1282 T12: 0.0404 REMARK 3 T13: 0.0655 T23: -0.1412 REMARK 3 L TENSOR REMARK 3 L11: 7.2839 L22: 9.4851 REMARK 3 L33: 9.0179 L12: -3.5213 REMARK 3 L13: 1.3069 L23: 3.0489 REMARK 3 S TENSOR REMARK 3 S11: -0.4514 S12: -0.7915 S13: -0.0998 REMARK 3 S21: -0.1211 S22: 0.5919 S23: -0.9792 REMARK 3 S31: -0.7485 S32: 0.9373 S33: -0.1885 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID -2 THROUGH 9 ) REMARK 3 ORIGIN FOR THE GROUP (A): -43.1586 6.3322 -21.5864 REMARK 3 T TENSOR REMARK 3 T11: 1.5772 T22: 1.5888 REMARK 3 T33: 1.7595 T12: 0.4466 REMARK 3 T13: -0.2871 T23: -0.2260 REMARK 3 L TENSOR REMARK 3 L11: 3.0388 L22: 3.0928 REMARK 3 L33: 3.4512 L12: -3.0995 REMARK 3 L13: 0.8097 L23: 0.1256 REMARK 3 S TENSOR REMARK 3 S11: -2.8700 S12: -1.1995 S13: 2.1922 REMARK 3 S21: 4.1920 S22: 2.0127 S23: -2.8839 REMARK 3 S31: -0.6933 S32: -1.4676 S33: 0.2264 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 7UDK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1000262669. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0329 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL CRYO-COOLED REMARK 200 SI(111) 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 : 6621 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.180 REMARK 200 RESOLUTION RANGE LOW (A) : 35.390 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.1 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.08023 REMARK 200 R SYM (I) : 0.08023 REMARK 200 FOR THE DATA SET : 14.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.29 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PREDICTED MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7, 10% W/V PEG6000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-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 85.43333 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 42.71667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 42.71667 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 85.43333 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: 1660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL 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 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 ASN A 40 30.03 -92.65 REMARK 500 ASN A 83 47.55 -106.80 REMARK 500 REMARK 500 REMARK: NULL DBREF 7UDK A 0 171 PDB 7UDK 7UDK 0 171 DBREF 7UDK B -2 9 PDB 7UDK 7UDK -2 9 SEQRES 1 A 172 ASP ARG GLU GLU ALA ALA PHE LEU ALA ALA SER ILE LEU SEQRES 2 A 172 ILE GLN HIS ALA HIS GLU GLN GLY LYS ASP ASP ARG GLU SEQRES 3 A 172 LEU GLU LYS ILE LEU GLU ILE ALA ILE ARG ILE LEU GLU SEQRES 4 A 172 LYS ASN GLY VAL ASP ARG GLU GLU ALA ALA PHE LEU ALA SEQRES 5 A 172 ALA SER ILE LEU ILE GLN HIS ALA HIS GLU GLN GLY LYS SEQRES 6 A 172 ASP ASP ARG GLU LEU GLU LYS ILE LEU GLU ILE ALA ILE SEQRES 7 A 172 ARG ILE LEU GLU LYS ASN GLY VAL ASP ARG GLU GLU ALA SEQRES 8 A 172 ALA PHE LEU ALA ALA SER ILE LEU ILE GLN HIS ALA HIS SEQRES 9 A 172 GLU GLN GLY LYS ASP ASP ARG GLU LEU GLU LYS ILE LEU SEQRES 10 A 172 GLU ILE ALA ILE ARG ILE LEU GLU LYS ASN GLY VAL ASP SEQRES 11 A 172 ARG GLU GLU ALA ALA PHE LEU ALA ALA SER ILE LEU ILE SEQRES 12 A 172 GLN HIS ALA HIS GLU GLN GLY LYS ASP ASP ARG GLU LEU SEQRES 13 A 172 GLU LYS ILE LEU GLU ILE ALA ILE ARG ILE LEU GLU LYS SEQRES 14 A 172 ASN GLY VAL SEQRES 1 B 12 LEU ARG PRO LEU ARG PRO LEU ARG PRO LEU ARG PRO HELIX 1 AA1 ASP A 0 GLY A 20 1 21 HELIX 2 AA2 ASP A 22 ASN A 40 1 19 HELIX 3 AA3 ASP A 43 GLN A 62 1 20 HELIX 4 AA4 ASP A 65 ASN A 83 1 19 HELIX 5 AA5 ASP A 86 GLY A 106 1 21 HELIX 6 AA6 ASP A 108 GLY A 127 1 20 HELIX 7 AA7 ASP A 129 GLN A 148 1 20 HELIX 8 AA8 ASP A 151 ASN A 169 1 19 CRYST1 70.780 70.780 128.150 90.00 90.00 120.00 P 32 2 1 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 0.014128 0.008157 0.000000 0.00000 SCALE2 0.000000 0.016314 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007803 0.00000