HEADER STRUCTURAL PROTEIN 22-DEC-17 6FDE TITLE CRYSTAL STRUCTURE OF THE HHD2 DOMAIN OF WHIRLIN : 3-HELIX CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: WHIRLIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: WHIRLIN DOMAIN HHD2 RESIDUES 420-499; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: WHRN, DFNB31, KIAA1526; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS USHER SYNDROME, SCAFFOLD PROTEIN, HEARING, DEAFNESS, STRUCTURAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.DELHOMMEL,F.CORDIER,F.SAUL,A.HAOUZ,N.WOLFF REVDAT 2 31-OCT-18 6FDE 1 JRNL REVDAT 1 08-AUG-18 6FDE 0 JRNL AUTH F.DELHOMMEL,F.CORDIER,F.SAUL,L.CHATAIGNER,A.HAOUZ,N.WOLFF JRNL TITL STRUCTURAL PLASTICITY OF THE HHD2 DOMAIN OF WHIRLIN. JRNL REF FEBS J. V. 285 3738 2018 JRNL REFN ISSN 1742-4658 JRNL PMID 30053338 JRNL DOI 10.1111/FEBS.14614 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 5583 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.850 REMARK 3 FREE R VALUE TEST SET COUNT : 550 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.07 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.66 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 1504 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2263 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1357 REMARK 3 BIN R VALUE (WORKING SET) : 0.2242 REMARK 3 BIN FREE R VALUE : 0.2467 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.77 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 147 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 538 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.07860 REMARK 3 B22 (A**2) : -4.07860 REMARK 3 B33 (A**2) : 8.15730 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.290 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.173 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.155 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.162 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.151 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 562 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 762 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 201 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 11 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 85 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 562 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 75 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 663 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 0.91 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.07 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.07 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 5.8468 13.7840 2.7010 REMARK 3 T TENSOR REMARK 3 T11: 0.0487 T22: -0.0452 REMARK 3 T33: 0.0314 T12: 0.0372 REMARK 3 T13: -0.0390 T23: -0.0453 REMARK 3 L TENSOR REMARK 3 L11: 2.6185 L22: 2.2990 REMARK 3 L33: 5.0504 L12: -0.9623 REMARK 3 L13: 2.2406 L23: -2.4673 REMARK 3 S TENSOR REMARK 3 S11: -0.1820 S12: -0.0752 S13: 0.2888 REMARK 3 S21: 0.0366 S22: -0.0290 S23: -0.1810 REMARK 3 S31: -0.0753 S32: -0.2009 S33: 0.2110 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6FDE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1200007887. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5620 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 34.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.50700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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 (%): 20.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA CIT 2-PROPANOLOH 20% W/VPEG4K REMARK 280 20% W:V, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 49.86600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 17.33400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 17.33400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.93300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 17.33400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 17.33400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.79900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 17.33400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 17.33400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 24.93300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 17.33400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 17.33400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.79900 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 49.86600 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 GLY A 415 REMARK 465 ALA A 416 REMARK 465 MET A 417 REMARK 465 GLY A 418 REMARK 465 SER A 419 REMARK 465 GLY A 420 REMARK 465 ASN A 421 REMARK 465 GLN A 422 REMARK 465 THR A 423 REMARK 465 ARG A 424 REMARK 465 ALA A 425 REMARK 465 LEU A 426 REMARK 465 LEU A 427 REMARK 465 ASP A 428 REMARK 465 ASP A 429 REMARK 465 GLN A 430 REMARK 465 ARG A 499 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 A 490 CG OD1 OD2 REMARK 470 ARG A 491 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 498 CG CD NE CZ NH1 NH2 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 GLU A 479 -60.58 -123.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6FDD RELATED DB: PDB REMARK 900 WHIRLIN DOMAIN HHD2. DBREF 6FDE A 420 499 UNP Q80VW5 WHRN_MOUSE 420 499 SEQADV 6FDE GLY A 415 UNP Q80VW5 EXPRESSION TAG SEQADV 6FDE ALA A 416 UNP Q80VW5 EXPRESSION TAG SEQADV 6FDE MET A 417 UNP Q80VW5 EXPRESSION TAG SEQADV 6FDE GLY A 418 UNP Q80VW5 EXPRESSION TAG SEQADV 6FDE SER A 419 UNP Q80VW5 EXPRESSION TAG SEQRES 1 A 85 GLY ALA MET GLY SER GLY ASN GLN THR ARG ALA LEU LEU SEQRES 2 A 85 ASP ASP GLN ALA ARG HIS LEU LEU THR GLU GLN GLU ARG SEQRES 3 A 85 ALA THR MET MET TYR TYR LEU ALA GLN TYR ARG GLY GLY SEQRES 4 A 85 THR ILE SER VAL GLU ALA MET VAL MET ALA LEU PHE GLU SEQRES 5 A 85 LEU LEU ASN THR HIS ALA LYS PHE SER LEU LEU SER GLU SEQRES 6 A 85 VAL ARG SER ILE ILE SER PRO GLN ASP LEU ASP ARG PHE SEQRES 7 A 85 ASP HIS LEU VAL LEU ARG ARG FORMUL 2 HOH *10(H2 O) HELIX 1 AA1 ALA A 431 GLY A 452 1 22 HELIX 2 AA2 SER A 456 GLU A 479 1 24 HELIX 3 AA3 VAL A 480 ILE A 484 5 5 HELIX 4 AA4 SER A 485 GLN A 487 5 3 HELIX 5 AA5 ASP A 488 ARG A 498 1 11 CRYST1 34.668 34.668 99.732 90.00 90.00 90.00 P 41 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 0.028845 0.000000 0.000000 0.00000 SCALE2 0.000000 0.028845 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010027 0.00000