10 20 30 40 50 60 70 80 2F4K - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL PROTEIN 23-NOV-05 2F4K
TITLE CHICKEN VILLIN SUBDOMAIN HP-35, K65(NLE), N68H, K70(NLE), TITLE 2 PH9
COMPND MOL_ID: 1; COMPND 2 MOLECULE: VILLIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 792-826; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN GALLUS SOURCE 4 GALLUS (CHICKEN).
KEYWDS VILLIN HEAD GROUP SUBDOMAIN, STRUCTURAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR T.K.CHIU,D.R.DAVIES,J.KUBELKA,J.HOFRICHTER,W.A.EATON
REVDAT 3 24-FEB-09 2F4K 1 VERSN REVDAT 2 13-JUN-06 2F4K 1 JRNL REVDAT 1 11-APR-06 2F4K 0
JRNL AUTH J.KUBELKA,T.K.CHIU,D.R.DAVIES,W.A.EATON, JRNL AUTH 2 J.HOFRICHTER JRNL TITL SUB-MICROSECOND PROTEIN FOLDING. JRNL REF J.MOL.BIOL. V. 359 546 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16643946 JRNL DOI 10.1016/J.JMB.2006.03.034
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.05 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.140 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.140 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.400 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 698 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 13042 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.131 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.131 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.158 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 502 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 9454 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 601 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 53 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 336.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 275.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 5 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 3238 REMARK 3 NUMBER OF RESTRAINTS : 4064 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.033 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.018 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.008 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.007 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.043 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.039 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.114 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STARTING MODEL WAS REFINED BY RIGID- REMARK 3 BODY AND TORSION-ANGLE REFINEMENT IN CNS. TWO DATASETS WERE REMARK 3 COLLECTED, ONE AT NIH AND OTHER BY MAIL-IN-CR AT APS BEAMLINE REMARK 3 22-ID AND FINALLY MERGED. ANISOTROPIC SCALING APPLIED BY THE REMARK 3 METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 REMARK 3 WHICH REDUCED FREE R USING SHELX. SHELXL PARAMETERS: DEFS 0.02 REMARK 3 0.02 0.01 0.04, SIMU 0.05, ISOR 0.2, HOPE, SWAT, ANIS, WGHT REMARK 3 0.25
REMARK 4 REMARK 4 2F4K COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-05. REMARK 100 THE RCSB ID CODE IS RCSB035444.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-05; 16-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 95; 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : APS; ROTATING ANODE REMARK 200 BEAMLINE : 22-ID; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00; 1.54 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13770 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.050 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.09 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.40100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: 1WY3 WITHOUT SOLVENT REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.82 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: INITIAL DROP CONTAINED 1UL 90MG/ML REMARK 280 PROTEIN IN 10MM TRIS (PH7.4) AND 7.5% V/V TRIFLUOROETHANOL REMARK 280 (TFE) AND 1UL RESERVOIR SOLUTION. PRECIPITANT IN RESERVOIR WAS REMARK 280 (INITIAL: 800MM AMSO4, 100MM BICINE (PH 9.0), 10% V/V TFE) AND REMARK 280 (FINAL: 1.6M AMSO4, 100MM BICINE (PH 9.0), 7.5% V/V TFE). REMARK 280 RESERVOIR SOLUTION WAS CHANGED FROM INITIAL TO FINAL AFTER ONE REMARK 280 WEEK.
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 37.54450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.54450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 9.83850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.95050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 9.83850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.95050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.54450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 9.83850 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 19.95050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 37.54450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 9.83850 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 19.95050 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: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 120 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 124 LIES ON A SPECIAL POSITION.
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE A 47 CB - CG - CD1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG A 55 NE - CZ - NH1 ANGL. DEV. = -5.2 DEGREES REMARK 500 PHE A 76 C - N - CA ANGL. DEV. = 22.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YRF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CHICKEN VILLIN SUBDOMAIN HP-35, N68H, REMARK 900 PH 6.7 REMARK 900 RELATED ID: 1YRI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CHICKEN VILLIN SUBDOMAIN HP-35, N68H, REMARK 900 PH 6.4 REMARK 900 RELATED ID: 1WY4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CHICKEN VILLIN SUBDOMAIN HP-35, REMARK 900 K65(NLE), N68H, PH 5.1 REMARK 900 RELATED ID: 1WY3 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CHICKEN VILLIN SUBDOMAIN HP-35, REMARK 900 K65(NLE), N68H, PH 7.0
DBREF 2F4K A 42 76 UNP P02640 VILI_CHICK 792 826
SEQADV 2F4K NLE A 65 UNP P02640 LYS 815 MODIFIED RESIDUE SEQADV 2F4K HIS A 68 UNP P02640 ASN 818 ENGINERED SEQADV 2F4K NLE A 70 UNP P02640 LYS 820 MODIFIED RESIDUE
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 TRP NLE GLN GLN SEQRES 3 A 35 HIS LEU NLE LYS GLU LYS GLY LEU PHE
MODRES 2F4K NLE A 65 LEU NORLEUCINE MODRES 2F4K NLE A 70 LEU NORLEUCINE
HET NLE A 65 19 HET NLE A 70 19
HETNAM NLE NORLEUCINE
FORMUL 1 NLE 2(C6 H13 N O2) FORMUL 2 HOH *52(H2 O)
HELIX 1 1 SER A 43 GLY A 52 1 10 HELIX 2 2 THR A 54 LEU A 61 1 8 HELIX 3 3 PRO A 62 GLY A 74 1 13
LINK C TRP A 64 N NLE A 65 1555 1555 1.32 LINK C NLE A 65 N GLN A 66 1555 1555 1.32 LINK C LEU A 69 N NLE A 70 1555 1555 1.32 LINK C NLE A 70 N LYS A 71 1555 1555 1.34
CRYST1 19.677 39.901 75.089 90.00 90.00 90.00 C 2 2 21 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 0.050821 0.000000 0.000000 0.00000
SCALE2 0.000000 0.025062 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013318 0.00000