PDB Short entry for 3TRW HEADER STRUCTURAL PROTEIN 11-SEP-11 3TRW TITLE CRYSTAL STRUCTURE OF RACEMIC VILLIN HEADPIECE SUBDOMAIN CRYSTALLIZED TITLE 2 IN SPACE GROUP P-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VILLIN-1; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: HEADPIECE SUBDOMAIN (UNP RESIDUES 792-826); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 4 ORGANISM_COMMON: CHICKEN; SOURCE 5 ORGANISM_TAXID: 9031 KEYWDS RACEMATE, QUASI-RACEMATE, D-AMINO ACIDS, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.E.MORTENSON,K.A.SATYSHUR,S.H.GELLMAN,K.T.FOREST REVDAT 4 13-SEP-23 3TRW 1 SEQADV REVDAT 3 22-FEB-12 3TRW 1 JRNL REVDAT 2 08-FEB-12 3TRW 1 JRNL REVDAT 1 25-JAN-12 3TRW 0 JRNL AUTH D.E.MORTENSON,K.A.SATYSHUR,I.A.GUZEI,K.T.FOREST,S.H.GELLMAN JRNL TITL QUASIRACEMIC CRYSTALLIZATION AS A TOOL TO ASSESS THE JRNL TITL 2 ACCOMMODATION OF NONCANONICAL RESIDUES IN NATIVELIKE PROTEIN JRNL TITL 3 CONFORMATIONS. JRNL REF J.AM.CHEM.SOC. V. 134 2473 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 22280019 JRNL DOI 10.1021/JA210045S REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 7112 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) : 0.294 REMARK 3 R VALUE (WORKING SET) : 0.291 REMARK 3 FREE R VALUE : 0.352 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 334 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4300 REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : 0.4190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 536 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 24.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.13000 REMARK 3 B22 (A**2) : -3.70000 REMARK 3 B33 (A**2) : -3.04000 REMARK 3 B12 (A**2) : -1.07000 REMARK 3 B13 (A**2) : -1.07000 REMARK 3 B23 (A**2) : -0.33000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.221 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.219 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.152 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.808 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 553 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 735 ; 1.352 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 68 ; 4.716 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 25 ;29.902 ;24.400 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 113 ;17.627 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ;10.387 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 79 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 401 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 34 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7073 5.6850 5.4935 REMARK 3 T TENSOR REMARK 3 T11: 0.0914 T22: 0.0514 REMARK 3 T33: 0.0063 T12: 0.0182 REMARK 3 T13: -0.0178 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 1.6777 L22: 6.6231 REMARK 3 L33: 3.0390 L12: 0.6452 REMARK 3 L13: -1.6020 L23: -3.7178 REMARK 3 S TENSOR REMARK 3 S11: 0.1510 S12: -0.1479 S13: -0.0762 REMARK 3 S21: -0.3432 S22: -0.2131 S23: -0.0130 REMARK 3 S31: 0.0500 S32: 0.2183 S33: 0.0621 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 1 D 34 REMARK 3 ORIGIN FOR THE GROUP (A): 12.0202 9.4911 24.6445 REMARK 3 T TENSOR REMARK 3 T11: 0.0398 T22: 0.1003 REMARK 3 T33: 0.0670 T12: -0.0009 REMARK 3 T13: 0.0065 T23: 0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.5255 L22: 7.9332 REMARK 3 L33: 4.8176 L12: -1.0918 REMARK 3 L13: 0.7980 L23: 2.8386 REMARK 3 S TENSOR REMARK 3 S11: 0.0569 S12: -0.0445 S13: 0.0708 REMARK 3 S21: -0.1588 S22: -0.1390 S23: -0.1226 REMARK 3 S31: 0.0492 S32: -0.2689 S33: 0.0822 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 3 U VALUES : RESIDUAL ONLY REMARK 3 STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS REMARK 4 REMARK 4 3TRW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067845. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.75 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7112 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 27.794 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 3.710 REMARK 200 R MERGE (I) : 0.07720 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.6600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.74 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29600 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.020 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: PDB ENTRY 1YRF REMARK 200 REMARK 200 REMARK: STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0 M AMMONIUM SULFATE, 6% REMARK 280 ISOPROPANOL, 8% GLYCEROL, PH 5.75, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K 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 2555 -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 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 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: D 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 PHE A 35 REMARK 465 PHE D 35 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TJW RELATED DB: PDB REMARK 900 RELATED ID: 3TRV RELATED DB: PDB REMARK 900 RELATED ID: 3TRY RELATED DB: PDB DBREF 3TRW A 1 35 UNP P02640 VILI_CHICK 792 826 DBREF 3TRW D 1 35 UNP P02640 VILI_CHICK 792 826 SEQADV 3TRW ALA A 23 UNP P02640 TRP 814 CONFLICT SEQADV 3TRW HIS A 27 UNP P02640 ASN 818 ENGINEERED MUTATION SEQADV 3TRW ALA D 23 UNP P02640 TRP 814 CONFLICT SEQADV 3TRW HIS D 27 UNP P02640 ASN 818 ENGINEERED MUTATION SEQRES 1 A 35 LEU SER ASP GLU ASP PHE LYS ALA VAL PHE GLY MET THR SEQRES 2 A 35 ARG SER ALA PHE ALA ASN LEU PRO LEU ALA LYS GLN GLN SEQRES 3 A 35 HIS LEU LYS LYS GLU LYS GLY LEU PHE SEQRES 1 D 35 LEU SER ASP GLU ASP PHE LYS ALA VAL PHE GLY MET THR SEQRES 2 D 35 ARG SER ALA PHE ALA ASN LEU PRO LEU ALA LYS GLN GLN SEQRES 3 D 35 HIS LEU LYS LYS GLU LYS GLY LEU PHE FORMUL 3 HOH *19(H2 O) HELIX 1 1 SER A 2 GLY A 11 1 10 HELIX 2 2 THR A 13 ALA A 18 1 6 HELIX 3 3 PRO A 21 GLY A 33 1 13 HELIX 4 4 SER D 2 GLY D 11 1 10 HELIX 5 5 THR D 13 ALA D 18 1 6 HELIX 6 6 PRO D 21 GLY D 33 1 13 CRYST1 28.380 31.730 36.750 90.12 99.61 96.52 P -1 4 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 0.035236 0.004028 0.006056 0.00000 SCALE2 0.000000 0.031721 0.000680 0.00000 SCALE3 0.000000 0.000000 0.027605 0.00000