HEADER STRUCTURAL PROTEIN 16-JUN-06 2DRX TITLE STRUCTURE ANALYSIS OF (POG)4-(LOG)2-(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: TWO LEU-HYP-GLY GUEST TRIPLETS SANDWICHED BY HOST SOURCE 4 PRO-HYP-GLY SEQUENCE; THIS HOST TRIPLET IS VERY POPULAR IN THE SOURCE 5 COLLAGEN SEQUENCE. KEYWDS COLLAGEN, TRIPLE HELIX, LEU, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.OKUYAMA REVDAT 4 25-OCT-23 2DRX 1 LINK REVDAT 3 24-FEB-09 2DRX 1 VERSN REVDAT 2 22-MAY-07 2DRX 1 JRNL REVDAT 1 24-APR-07 2DRX 0 JRNL AUTH K.OKUYAMA,H.NARITA,T.KAWAGUCHI,K.NOGUCHI,Y.TANAKA,N.NISHINO JRNL TITL UNIQUE SIDE CHAIN CONFORMATION OF A LEU RESIDUE IN A JRNL TITL 2 TRIPLE-HELICAL STRUCTURE JRNL REF BIOPOLYMERS V. 86 212 2007 JRNL REFN ISSN 0006-3525 JRNL PMID 17373653 JRNL DOI 10.1002/BIP.20724 REMARK 2 REMARK 2 RESOLUTION. 1.40 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.5 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) : 0.160 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 657 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 10254 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.152 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 8862 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 558 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 170 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 720.50 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 482.50 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4655 REMARK 3 NUMBER OF RESTRAINTS : 5584 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) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.046 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.052 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.009 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.003 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.027 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.038 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: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY ? REMARK 4 REMARK 4 2DRX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000025770. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10986 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.29400 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 (%): 32.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13.5% PEG 2000, 0.05M CITRATE BUFFER, REMARK 280 PH 6.0, VAPOR DIFFUSION, HANGING DROP, 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 11.37550 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: 5040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 HYP A 29 REMARK 465 GLY A 30 REMARK 465 PRO B 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2DRT RELATED DB: PDB REMARK 900 SIMILAR SEQUENCE WITH ONE LOG TRIPLET REMARK 900 RELATED ID: 1V4F RELATED DB: PDB REMARK 900 SIMILAR SEQUENCE WITH NO LOG TRIPLET DBREF 2DRX A 1 30 PDB 2DRX 2DRX 1 30 DBREF 2DRX B 1 30 PDB 2DRX 2DRX 1 30 DBREF 2DRX C 1 30 PDB 2DRX 2DRX 1 30 SEQRES 1 A 30 PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY LEU SEQRES 2 A 30 HYP GLY LEU HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP SEQRES 3 A 30 GLY PRO HYP GLY SEQRES 1 B 30 PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY LEU SEQRES 2 B 30 HYP GLY LEU HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP SEQRES 3 B 30 GLY PRO HYP GLY SEQRES 1 C 30 PRO HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP GLY LEU SEQRES 2 C 30 HYP GLY LEU HYP GLY PRO HYP GLY PRO HYP GLY PRO HYP SEQRES 3 C 30 GLY PRO HYP GLY MODRES 2DRX HYP A 2 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP A 5 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP A 8 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP A 11 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP A 14 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP A 17 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP A 20 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP A 23 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP A 26 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP B 2 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP B 5 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP B 8 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP B 11 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP B 14 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP B 17 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP B 20 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP B 23 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP B 26 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP B 29 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP C 2 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP C 5 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP C 8 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP C 11 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP C 14 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP C 17 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP C 20 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP C 23 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP C 26 PRO 4-HYDROXYPROLINE MODRES 2DRX HYP C 29 PRO 4-HYDROXYPROLINE HET HYP A 2 8 HET HYP A 5 8 HET HYP A 8 8 HET HYP A 11 8 HET HYP A 14 8 HET HYP A 17 8 HET HYP A 20 8 HET HYP A 23 8 HET HYP A 26 8 HET HYP B 2 8 HET HYP B 5 8 HET HYP B 8 8 HET HYP B 11 8 HET HYP B 14 8 HET HYP B 17 8 HET HYP B 20 8 HET HYP B 23 8 HET HYP B 26 8 HET HYP B 29 8 HET HYP C 2 8 HET HYP C 5 8 HET HYP C 8 8 HET HYP C 11 8 HET HYP C 14 8 HET HYP C 17 8 HET HYP C 20 8 HET HYP C 23 8 HET HYP C 26 8 HET HYP C 29 8 HETNAM HYP 4-HYDROXYPROLINE HETSYN HYP HYDROXYPROLINE FORMUL 1 HYP 29(C5 H9 N O3) FORMUL 4 HOH *170(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 1.32 LINK C PRO A 4 N HYP A 5 1555 1555 1.32 LINK C HYP A 5 N GLY A 6 1555 1555 1.33 LINK C PRO A 7 N HYP A 8 1555 1555 1.33 LINK C HYP A 8 N GLY A 9 1555 1555 1.33 LINK C PRO A 10 N HYP A 11 1555 1555 1.32 LINK C HYP A 11 N GLY A 12 1555 1555 1.32 LINK C LEU A 13 N HYP A 14 1555 1555 1.33 LINK C HYP A 14 N GLY A 15 1555 1555 1.33 LINK C LEU A 16 N HYP A 17 1555 1555 1.33 LINK C HYP A 17 N GLY A 18 1555 1555 1.32 LINK C PRO A 19 N HYP A 20 1555 1555 1.33 LINK C HYP A 20 N GLY A 21 1555 1555 1.34 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 A 25 N HYP A 26 1555 1555 1.33 LINK C HYP A 26 N GLY A 27 1555 1555 1.32 LINK C HYP B 2 N GLY B 3 1555 1555 1.33 LINK C PRO B 4 N HYP B 5 1555 1555 1.32 LINK C HYP B 5 N GLY B 6 1555 1555 1.33 LINK C PRO B 7 N HYP B 8 1555 1555 1.33 LINK C HYP B 8 N GLY B 9 1555 1555 1.34 LINK C PRO B 10 N HYP B 11 1555 1555 1.32 LINK C HYP B 11 N GLY B 12 1555 1555 1.35 LINK C LEU B 13 N HYP B 14 1555 1555 1.32 LINK C HYP B 14 N GLY B 15 1555 1555 1.34 LINK C LEU B 16 N HYP B 17 1555 1555 1.32 LINK C HYP B 17 N GLY B 18 1555 1555 1.31 LINK C PRO B 19 N HYP B 20 1555 1555 1.33 LINK C HYP B 20 N GLY B 21 1555 1555 1.34 LINK C PRO B 22 N HYP B 23 1555 1555 1.34 LINK C HYP B 23 N GLY B 24 1555 1555 1.33 LINK C PRO B 25 N HYP B 26 1555 1555 1.33 LINK C HYP B 26 N GLY B 27 1555 1555 1.32 LINK C PRO B 28 N HYP B 29 1555 1555 1.33 LINK C HYP B 29 N GLY B 30 1555 1555 1.33 LINK C PRO C 1 N HYP C 2 1555 1555 1.33 LINK C HYP C 2 N GLY C 3 1555 1555 1.32 LINK C PRO C 4 N HYP C 5 1555 1555 1.32 LINK C HYP C 5 N GLY C 6 1555 1555 1.34 LINK C PRO C 7 N HYP C 8 1555 1555 1.34 LINK C HYP C 8 N GLY C 9 1555 1555 1.32 LINK C PRO C 10 N HYP C 11 1555 1555 1.32 LINK C HYP C 11 N GLY C 12 1555 1555 1.32 LINK C LEU C 13 N HYP C 14 1555 1555 1.33 LINK C HYP C 14 N GLY C 15 1555 1555 1.34 LINK C LEU 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 1.34 LINK C PRO C 22 N HYP C 23 1555 1555 1.32 LINK C HYP C 23 N GLY C 24 1555 1555 1.32 LINK C PRO C 25 N HYP C 26 1555 1555 1.31 LINK C HYP C 26 N GLY C 27 1555 1555 1.33 LINK C PRO C 28 N HYP C 29 1555 1555 1.34 LINK C HYP C 29 N GLY C 30 1555 1555 1.33 CRYST1 29.894 22.751 46.372 90.00 107.62 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 0.033452 0.000000 0.010624 0.00000 SCALE2 0.000000 0.043954 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022626 0.00000