HEADER STRUCTURAL PROTEIN 03-DEC-03 1V6Q TITLE CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES WITH PRO-HYP-GLY TITLE 2 SEQUENCE AT 1.3 A COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN LIKE PEPTIDE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: COLLAGEN LIKE PEPTIDE; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: COLLAGEN LIKE PEPTIDE; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: (PRO-HYP-GLY) TRIPLET IS VERY POPULAR IN COLLAGEN SOURCE 4 SEQUENCE; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: (PRO-HYP-GLY) TRIPLET IS VERY POPULAR IN COLLAGEN SOURCE 8 SEQUENCE; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: (PRO-HYP-GLY) TRIPLET IS VERY POPULAR IN COLLAGEN SOURCE 12 SEQUENCE KEYWDS COLLAGEN, TRIPLE-HELIX, MODEL PEPTIDE, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.OKUYAMA,C.HONGO,R.FUKUSHIMA,G.WU,H.NARITA,K.NOGUCHI,Y.TANAKA, AUTHOR 2 N.NISHINO REVDAT 6 03-APR-24 1V6Q 1 REMARK REVDAT 5 27-DEC-23 1V6Q 1 LINK REVDAT 4 25-DEC-13 1V6Q 1 REMARK VERSN REVDAT 3 24-FEB-09 1V6Q 1 VERSN REVDAT 2 21-DEC-04 1V6Q 1 JRNL REVDAT 1 03-AUG-04 1V6Q 0 JRNL AUTH K.OKUYAMA,C.HONGO,R.FUKUSHIMA,G.WU,H.NARITA,K.NOGUCHI, JRNL AUTH 2 Y.TANAKA,N.NISHINO JRNL TITL CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES WITH JRNL TITL 2 PRO-HYP-GLY REPEATING SEQUENCE AT 1.26 A RESOLUTION: JRNL TITL 3 IMPLICATIONS FOR PROLINE RING PUCKERING JRNL REF BIOPOLYMERS V. 76 367 2004 JRNL REFN ISSN 0006-3525 JRNL PMID 15386273 JRNL DOI 10.1002/BIP.20107 REMARK 2 REMARK 2 RESOLUTION. 1.25 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) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.1 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) : 0.135 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 186 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 3733 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)) : 0.127 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.180 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 157 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 3142 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 133 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 42 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 175.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 112.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1368 REMARK 3 NUMBER OF RESTRAINTS : 1698 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.018 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.093 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.033 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.014 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.037 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: THE POLYMER STRUCTURE CAN BE GENERATED REMARK 3 FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE (0 0 1) REMARK 3 TRANSLATION USING FRACTIONAL COORDINATES. REMARK 4 REMARK 4 1V6Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000006275. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL 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) : 1.00 REMARK 200 MONOCHROMATOR : FIXED-EXIT DOUBLE CRYSTAL REMARK 200 OPTICS : 1-M-LONG BENT-CYLINDER MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3768 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 19.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHELX REMARK 200 STARTING MODEL: (PRO-HYP-GLY)10 STRUCTURE REPORTED IN V.NAGARAJAN, REMARK 200 S.KAMITORI AND K.OKUYAMA, J.BIOCHEM., 125, 310 (1999). REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 200, ACETIC ACID, SODIUM AZIDE, REMARK 280 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 13.38750 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 300 REMARK: THE ENTIRE 33 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM REMARK 300 THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING REMARK 300 TRANSLATIONS (USING FRACTIONAL COORDINATES): REMARK 300 REMARK 300 CHAIN A: TRANSLATE RESIDUES 104-109 BY (001), AND REMARK 300 RESIDUES 103-109 BY (002), (003), (004)(005). REMARK 300 CHAIN B: TRANSLATE RESIDUES 204 - 208 BY (001), AND REMARK 300 RESIDUES 202-208 BY (002), (003), (004) AND REMARK 300 RESIDUE 202-206 BY (005). REMARK 300 CHAIN C: TRANSLATE RESIDUES 301 - 307 BY (001), (002), REMARK 300 (003) (004), AND RESIDUES 301-306 BY (005). REMARK 300 REMARK 300 THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 99 RESIDUES, REMARK 300 33 IN EACH CHAIN. 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: HEXAMERIC 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 350 BIOMT1 2 1.000000 0.000000 0.000000 -5.76842 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 19.15425 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 C GLY A 109 N PRO C 301 1556 1.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CAG RELATED DB: PDB REMARK 900 SIMILAR SEQUENCE REMARK 900 RELATED ID: 1V4F RELATED DB: PDB REMARK 900 THE SAME PEPTIDE MEASURED AT 100K REMARK 900 RELATED ID: 1V7H RELATED DB: PDB REMARK 900 HOLOMOLOGOUS PEPTIDE MEASURED AT 100K DBREF 1V6Q A 103 109 PDB 1V6Q 1V6Q 103 109 DBREF 1V6Q B 202 208 PDB 1V6Q 1V6Q 202 208 DBREF 1V6Q C 301 307 PDB 1V6Q 1V6Q 301 307 SEQRES 1 A 7 GLY PRO HYP GLY PRO HYP GLY SEQRES 1 B 7 HYP GLY PRO HYP GLY PRO HYP SEQRES 1 C 7 PRO HYP GLY PRO HYP GLY PRO MODRES 1V6Q HYP A 105 PRO 4-HYDROXYPROLINE MODRES 1V6Q HYP A 108 PRO 4-HYDROXYPROLINE MODRES 1V6Q HYP B 202 PRO 4-HYDROXYPROLINE MODRES 1V6Q HYP B 205 PRO 4-HYDROXYPROLINE MODRES 1V6Q HYP B 208 PRO 4-HYDROXYPROLINE MODRES 1V6Q HYP C 302 PRO 4-HYDROXYPROLINE MODRES 1V6Q HYP C 305 PRO 4-HYDROXYPROLINE HET HYP A 105 8 HET HYP A 108 8 HET HYP B 202 8 HET HYP B 205 8 HET HYP B 208 8 HET HYP C 302 8 HET HYP C 305 8 HETNAM HYP 4-HYDROXYPROLINE HETSYN HYP HYDROXYPROLINE FORMUL 1 HYP 7(C5 H9 N O3) FORMUL 4 HOH *42(H2 O) LINK N GLY A 103 C HYP B 208 1556 1555 1.34 LINK C PRO A 104 N HYP A 105 1555 1555 1.32 LINK C HYP A 105 N GLY A 106 1555 1555 1.32 LINK C PRO A 107 N HYP A 108 1555 1555 1.33 LINK C HYP A 108 N GLY A 109 1555 1555 1.35 LINK C HYP B 202 N GLY B 203 1555 1555 1.33 LINK N HYP B 202 C PRO C 307 1555 1554 1.33 LINK C PRO B 204 N HYP B 205 1555 1555 1.33 LINK C HYP B 205 N GLY B 206 1555 1555 1.32 LINK C PRO B 207 N HYP B 208 1555 1555 1.32 LINK C PRO C 301 N HYP C 302 1555 1555 1.32 LINK C HYP C 302 N GLY C 303 1555 1555 1.33 LINK C PRO C 304 N HYP C 305 1555 1555 1.33 LINK C HYP C 305 N GLY C 306 1555 1555 1.32 CRYST1 14.051 26.775 20.004 90.00 106.76 90.00 P 1 21 1 2 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 0.071169 0.000000 0.021433 0.00000 SCALE2 0.000000 0.037348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.052208 0.00000