HEADER STRUCTURAL PROTEIN 04-FEB-05 1WY4 TITLE CHICKEN VILLIN SUBDOMAIN HP-35, K65(NLE), N68H, PH5.1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VILLIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: VHP; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: SYNTHETIC PEPTIDE, SEQUENCE CORRESPONDS TO CHICKEN SOURCE 4 VILLIN RESIDUES 792-826, RESIDUE 65 IS NORLEUCINE (LYSINE WITHOUT SOURCE 5 TERMINAL NH3 GROUP) KEYWDS VILLIN HEADGROUP SUBDOMAIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.K.CHIU,J.KUBELKA,R.HERBST-IRMER,W.A.EATON,J.HOFRICHTER,D.R.DAVIES REVDAT 9 13-NOV-24 1WY4 1 REMARK REVDAT 8 15-NOV-23 1WY4 1 REMARK REVDAT 7 23-AUG-23 1WY4 1 REMARK REVDAT 6 20-OCT-21 1WY4 1 REMARK SEQADV LINK REVDAT 5 11-OCT-17 1WY4 1 REMARK REVDAT 4 24-FEB-09 1WY4 1 VERSN REVDAT 3 21-JUN-05 1WY4 1 JRNL REVDAT 2 31-MAY-05 1WY4 1 JRNL REVDAT 1 03-MAY-05 1WY4 0 JRNL AUTH T.K.CHIU,J.KUBELKA,R.HERBST-IRMER,W.A.EATON,J.HOFRICHTER, JRNL AUTH 2 D.R.DAVIES JRNL TITL HIGH-RESOLUTION X-RAY CRYSTAL STRUCTURES OF THE VILLIN JRNL TITL 2 HEADPIECE SUBDOMAIN, AN ULTRAFAST FOLDING PROTEIN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 102 7517 2005 JRNL REFN ISSN 0027-8424 JRNL PMID 15894611 JRNL DOI 10.1073/PNAS.0502495102 REMARK 2 REMARK 2 RESOLUTION. 1.55 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.177 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 349 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 4299 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.176 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 346 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 4296 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 287 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 ANGLE DISTANCES (A) : 0.020 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.020 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.150 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.150 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.020 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUE 65 IS NORLEUCINE (LYSINE REMARK 3 WITHOUT TERMINAL NH3) SHELX: DEFS 0.02 0.15 0.01, SIMU 0.15, REMARK 3 ISOR 0.1, SWAT, BASF REMARK 4 REMARK 4 1WY4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-FEB-05. REMARK 100 THE DEPOSITION ID IS D_1000024140. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-04 REMARK 200 TEMPERATURE (KELVIN) : 95.0 REMARK 200 PH : 5.10 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 4299 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 26.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06600 REMARK 200 FOR THE DATA SET : 38.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 58.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.15300 REMARK 200 FOR SHELL : 14.20 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: 1YRF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1UL 50MG/ML PEPTIDE PLUS 1UL (200MM REMARK 280 AMCITRATE, 20% PEF3350), PH 5.1, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K, PH 5.10 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 37.68950 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 37.68950 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 9.86000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 20.11250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 9.86000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 20.11250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.68950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 9.86000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 20.11250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 37.68950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 9.86000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 20.11250 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 A1034 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 ARG A 55 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 100 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 IOD A 99 I REMARK 620 2 HOH A1007 O 132.9 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 98 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IOD A 99 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 100 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YRF RELATED DB: PDB REMARK 900 RELATED ID: 1YRI RELATED DB: PDB REMARK 900 RELATED ID: 1WY3 RELATED DB: PDB DBREF 1WY4 A 42 76 UNP P02640 VILI_CHICK 792 826 SEQADV 1WY4 NLE A 65 UNP P02640 LYS 815 ENGINEERED MUTATION SEQADV 1WY4 HIS A 68 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 TRP NLE GLN GLN SEQRES 3 A 35 HIS LEU LYS LYS GLU LYS GLY LEU PHE MODRES 1WY4 NLE A 65 LEU NORLEUCINE HET NLE A 65 8 HET IOD A 98 1 HET IOD A 99 1 HET NA A 100 1 HETNAM NLE NORLEUCINE HETNAM IOD IODIDE ION HETNAM NA SODIUM ION FORMUL 1 NLE C6 H13 N O2 FORMUL 2 IOD 2(I 1-) FORMUL 4 NA NA 1+ FORMUL 5 HOH *36(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 1.35 LINK C NLE A 65 N GLN A 66 1555 1555 1.32 LINK I IOD A 99 NA NA A 100 1555 1555 2.22 LINK NA NA A 100 O HOH A1007 1555 1655 2.06 SITE 1 AC1 2 LYS A 48 ARG A 55 SITE 1 AC2 2 GLN A 67 NA A 100 SITE 1 AC3 3 SER A 56 IOD A 99 HOH A1007 CRYST1 19.720 40.225 75.379 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 0.050710 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024860 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013266 0.00000