HEADER STRUCTURAL PROTEIN 06-DEC-13 3WN8 TITLE CRYSTAL STRUCTURE OF COLLAGEN-MODEL PEPTIDE, (POG)3-PRG-(POG)4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN-LIKE PEPTIDE; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS PEPTIDE APPEARS MOST FREQUENTLY IN NATIVE SOURCE 4 COLLAGEN. KEYWDS COLLAGEN-HELIX, HSP47 BINDING, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.OKUYAMA,M.HAGA,K.NOGUCHI,T.TANAKA REVDAT 1 13-AUG-14 3WN8 0 JRNL AUTH K.OKUYAMA,M.HAGA,K.NOGUCHI,T.TANAKA JRNL TITL PREFERRED SIDE-CHAIN CONFORMATION OF ARGININE RESIDUES IN A JRNL TITL 2 TRIPLE-HELICAL STRUCTURE. JRNL REF BIOPOLYMERS V. 101 1000 2014 JRNL REFN ISSN 0006-3525 JRNL PMID 24615532 JRNL DOI 10.1002/BIP.22478 REMARK 2 REMARK 2 RESOLUTION. 1.45 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.0 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) : 0.141 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 369 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 7177 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)) : 0.137 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 342 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 6776 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 463 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 591.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 402.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 2 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 2415 REMARK 3 NUMBER OF RESTRAINTS : 2138 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.057 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.044 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.006 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.035 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 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: NULL REMARK 4 REMARK 4 3WN8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-DEC-13. REMARK 100 THE RCSB ID CODE IS RCSB096547. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL40B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7224 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 8.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: X-PLOR REMARK 200 STARTING MODEL: PDB ENTRY 1V4F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 % PEG 4000, 0.05M TRIS-HCL, 0.005M REMARK 280 LITHIUM SULFATE, PH 7.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 9.78350 REMARK 290 SMTRY3 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLY B 24 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 B 11 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 11 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3B0S RELATED DB: PDB REMARK 900 THE SIMILAR COLLAGEN-LIKE PEPTIDE DBREF 3WN8 A 1 24 PDB 3WN8 3WN8 1 24 DBREF 3WN8 B 1 24 PDB 3WN8 3WN8 1 24 DBREF 3WN8 C 1 24 PDB 3WN8 3WN8 1 24 SEQRES 1 A 24 PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO ARG GLY PRO SEQRES 2 A 24 HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY SEQRES 1 B 24 PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO ARG GLY PRO SEQRES 2 B 24 HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY SEQRES 1 C 24 PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO ARG GLY PRO SEQRES 2 C 24 HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY MODRES 3WN8 HYP A 2 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP A 5 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP A 8 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP A 14 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP A 17 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP A 20 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP A 23 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP B 2 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP B 5 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP B 8 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP B 14 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP B 17 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP B 20 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP B 23 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP C 2 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP C 5 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP C 8 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP C 14 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP C 17 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP C 20 PRO 4-HYDROXYPROLINE MODRES 3WN8 HYP C 23 PRO 4-HYDROXYPROLINE HET HYP A 2 8 HET HYP A 5 8 HET HYP A 8 8 HET HYP A 14 8 HET HYP A 17 8 HET HYP A 20 8 HET HYP A 23 8 HET HYP B 2 8 HET HYP B 5 8 HET HYP B 8 8 HET HYP B 14 8 HET HYP B 17 8 HET HYP B 20 8 HET HYP B 23 8 HET HYP C 2 8 HET HYP C 5 8 HET HYP C 8 8 HET HYP C 14 8 HET HYP C 17 8 HET HYP C 20 8 HET HYP C 23 8 HETNAM HYP 4-HYDROXYPROLINE HETSYN HYP HYDROXYPROLINE FORMUL 1 HYP 21(C5 H9 N O3) FORMUL 4 HOH *129(H2 O) LINK C PRO A 1 N HYP A 2 1555 1555 1.33 LINK C HYP A 2 N GLY A 3 1555 1555 1.33 LINK C PRO A 4 N HYP A 5 1555 1555 1.34 LINK C HYP A 5 N GLY A 6 1555 1555 1.33 LINK C PRO A 7 N HYP A 8 1555 1555 1.31 LINK C HYP A 8 N GLY A 9 1555 1555 1.32 LINK C PRO A 13 N HYP A 14 1555 1555 1.34 LINK C HYP A 14 N GLY A 15 1555 1555 1.34 LINK C PRO A 16 N HYP A 17 1555 1555 1.34 LINK C HYP A 17 N GLY A 18 1555 1555 1.34 LINK C PRO A 19 N HYP A 20 1555 1555 1.34 LINK C HYP A 20 N GLY A 21 1555 1555 1.33 LINK C PRO A 22 N HYP A 23 1555 1555 1.32 LINK C HYP A 23 N GLY A 24 1555 1555 1.33 LINK C PRO B 1 N HYP B 2 1555 1555 1.33 LINK C HYP B 2 N GLY B 3 1555 1555 1.34 LINK C PRO B 4 N HYP B 5 1555 1555 1.33 LINK C HYP B 5 N GLY B 6 1555 1555 1.33 LINK C PRO B 7 N HYP B 8 1555 1555 1.32 LINK C HYP B 8 N GLY B 9 1555 1555 1.33 LINK C PRO B 13 N HYP B 14 1555 1555 1.32 LINK C HYP B 14 N GLY B 15 1555 1555 1.33 LINK C PRO B 16 N HYP B 17 1555 1555 1.33 LINK C HYP B 17 N GLY B 18 1555 1555 1.33 LINK C PRO B 19 N HYP B 20 1555 1555 1.32 LINK C HYP B 20 N GLY B 21 1555 1555 1.33 LINK C PRO B 22 N HYP B 23 1555 1555 1.34 LINK C PRO C 1 N HYP C 2 1555 1555 1.32 LINK C HYP C 2 N GLY C 3 1555 1555 1.34 LINK C PRO C 4 N HYP C 5 1555 1555 1.33 LINK C HYP C 5 N GLY C 6 1555 1555 1.34 LINK C PRO C 7 N HYP C 8 1555 1555 1.33 LINK C HYP C 8 N GLY C 9 1555 1555 1.32 LINK C PRO C 13 N HYP C 14 1555 1555 1.32 LINK C HYP C 14 N GLY C 15 1555 1555 1.34 LINK C PRO C 16 N HYP C 17 1555 1555 1.32 LINK C HYP C 17 N GLY C 18 1555 1555 1.33 LINK C PRO C 19 N HYP C 20 1555 1555 1.33 LINK C HYP C 20 N GLY C 21 1555 1555 1.33 LINK C PRO C 22 N HYP C 23 1555 1555 1.33 LINK C HYP C 23 N GLY C 24 1555 1555 1.32 CRYST1 23.285 19.567 49.022 90.00 94.51 90.00 P 1 21 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 0.042946 0.000000 0.003388 0.00000 SCALE2 0.000000 0.051106 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020462 0.00000 MASTER 205 0 21 0 0 0 0 6 0 0 0 6 END