HEADER STRUCTURAL PROTEIN 06-MAR-09 3A08 TITLE STRUCTURE OF (PPG)4-OOG-(PPG)4, MONOCLINIC, TWINNED CRYSTAL COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN-LIKE PEPTIDE; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS PEPTIDE WAS CHEMICALLY SYSTHESIZED. KEYWDS COLLAGEN HELIX, HOST-GUEST PEPTIDE, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.OKUYAMA,T.MORIMOTO,G.WU,K.NOGUCHI,K.MIZUNO,H.P.BACHINGER REVDAT 3 01-NOV-23 3A08 1 LINK REVDAT 2 17-SEP-14 3A08 1 JRNL VERSN REVDAT 1 12-JAN-10 3A08 0 JRNL AUTH K.OKUYAMA,T.MORIMOTO,H.NARITA,T.KAWAGUCHI,K.MIZUNO, JRNL AUTH 2 H.P.BACHINGER,G.WU,K.NOGUCHI JRNL TITL TWO CRYSTAL MODIFICATIONS OF JRNL TITL 2 (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4 REVEAL THE JRNL TITL 3 PUCKERING PREFERENCE OF HYP(X) IN THE HYP(X):HYP(Y) AND JRNL TITL 4 HYP(X):PRO(Y) STACKING PAIRS IN COLLAGEN HELICES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 66 88 2010 JRNL REFN ISSN 0907-4449 JRNL PMID 20057053 JRNL DOI 10.1107/S0907444909046642 REMARK 2 REMARK 2 RESOLUTION. 1.22 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) : 1.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 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) : 0.139 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1627 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL 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)) : 0.135 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)) : 26672 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 859 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 239 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1098.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 793.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 9886 REMARK 3 NUMBER OF RESTRAINTS : 13177 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.030 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) : 0.073 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.061 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.009 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.058 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.103 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 STRUCTURE WAS ANALYZED AGAINST REMARK 3 DETWINNED DIFFRACTION DATA. REMARK 4 REMARK 4 3A08 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000028647. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-04 REMARK 200 TEMPERATURE (KELVIN) : 95.0 REMARK 200 PH : 5.6 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 : 1.1-M-LONG BENT-PLANE 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 : 32577 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.220 REMARK 200 RESOLUTION RANGE LOW (A) : 26.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.520 REMARK 200 R MERGE (I) : 0.08200 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) : 1.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.79 REMARK 200 R MERGE FOR SHELL (I) : 0.28700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 2CUO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16.25%(W/V) PEG 1000, 0.05M ACETATE REMARK 280 BUFFER, PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K 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 13.33400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 3900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 4080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 A 24 REMARK 465 PRO A 25 REMARK 465 PRO A 26 REMARK 465 GLY A 27 REMARK 465 GLY B 24 REMARK 465 PRO B 25 REMARK 465 PRO B 26 REMARK 465 GLY B 27 REMARK 465 PRO C 1 REMARK 465 PRO C 2 REMARK 465 PRO C 26 REMARK 465 GLY C 27 REMARK 465 PRO D 1 REMARK 465 PRO D 2 REMARK 465 PRO E 1 REMARK 465 PRO E 2 REMARK 465 GLY E 27 REMARK 465 PRO F 1 REMARK 465 PRO F 2 REMARK 465 GLY F 3 REMARK 465 PRO F 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2D3H RELATED DB: PDB REMARK 900 THE STRUCTURE WAS REFINED AGAINST THE SAME INTENSITIES WITH THE REMARK 900 TWINNED DATA. REMARK 900 RELATED ID: 2CUO RELATED DB: PDB REMARK 900 THE SIMILAR COLLAGEN-LIKE PEPTIDE. REMARK 900 RELATED ID: 2D3F RELATED DB: PDB REMARK 900 THE RELATED HOST-GUEST PEPTIDE. REMARK 900 RELATED ID: 1X1K RELATED DB: PDB REMARK 900 THE RELATED HOST-GUEST PEPTIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE ADOPTS TRIPLE-HELICAL STRUCTURE SIMILAR TO THE REMARK 999 COLLAGEN-HELIX. DBREF 3A08 A 1 27 PDB 3A08 3A08 1 27 DBREF 3A08 B 1 27 PDB 3A08 3A08 1 27 DBREF 3A08 C 1 27 PDB 3A08 3A08 1 27 DBREF 3A08 D 1 27 PDB 3A08 3A08 1 27 DBREF 3A08 E 1 27 PDB 3A08 3A08 1 27 DBREF 3A08 F 1 27 PDB 3A08 3A08 1 27 SEQRES 1 A 27 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY HYP SEQRES 2 A 27 HYP GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 A 27 GLY SEQRES 1 B 27 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY HYP SEQRES 2 B 27 HYP GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 B 27 GLY SEQRES 1 C 27 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY HYP SEQRES 2 C 27 HYP GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 C 27 GLY SEQRES 1 D 27 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY HYP SEQRES 2 D 27 HYP GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 D 27 GLY SEQRES 1 E 27 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY HYP SEQRES 2 E 27 HYP GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 E 27 GLY SEQRES 1 F 27 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY HYP SEQRES 2 F 27 HYP GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 F 27 GLY MODRES 3A08 HYP A 13 PRO 4-HYDROXYPROLINE MODRES 3A08 HYP A 14 PRO 4-HYDROXYPROLINE MODRES 3A08 HYP B 13 PRO 4-HYDROXYPROLINE MODRES 3A08 HYP B 14 PRO 4-HYDROXYPROLINE MODRES 3A08 HYP C 13 PRO 4-HYDROXYPROLINE MODRES 3A08 HYP C 14 PRO 4-HYDROXYPROLINE MODRES 3A08 HYP D 13 PRO 4-HYDROXYPROLINE MODRES 3A08 HYP D 14 PRO 4-HYDROXYPROLINE MODRES 3A08 HYP E 13 PRO 4-HYDROXYPROLINE MODRES 3A08 HYP E 14 PRO 4-HYDROXYPROLINE MODRES 3A08 HYP F 13 PRO 4-HYDROXYPROLINE MODRES 3A08 HYP F 14 PRO 4-HYDROXYPROLINE HET HYP A 13 8 HET HYP A 14 8 HET HYP B 13 8 HET HYP B 14 8 HET HYP C 13 8 HET HYP C 14 8 HET HYP D 13 8 HET HYP D 14 8 HET HYP E 13 8 HET HYP E 14 8 HET HYP F 13 8 HET HYP F 14 8 HETNAM HYP 4-HYDROXYPROLINE HETSYN HYP HYDROXYPROLINE FORMUL 1 HYP 12(C5 H9 N O3) FORMUL 7 HOH *239(H2 O) LINK C GLY A 12 N HYP A 13 1555 1555 1.34 LINK C HYP A 13 N HYP A 14 1555 1555 1.34 LINK C HYP A 14 N GLY A 15 1555 1555 1.32 LINK C GLY B 12 N HYP B 13 1555 1555 1.35 LINK C HYP B 13 N HYP B 14 1555 1555 1.33 LINK C HYP B 14 N GLY B 15 1555 1555 1.32 LINK C GLY C 12 N HYP C 13 1555 1555 1.35 LINK C HYP 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 GLY D 12 N HYP D 13 1555 1555 1.36 LINK C HYP D 13 N HYP D 14 1555 1555 1.33 LINK C HYP D 14 N GLY D 15 1555 1555 1.34 LINK C GLY E 12 N HYP E 13 1555 1555 1.32 LINK C HYP E 13 N HYP E 14 1555 1555 1.32 LINK C HYP E 14 N GLY E 15 1555 1555 1.36 LINK C GLY F 12 N HYP F 13 1555 1555 1.32 LINK C HYP F 13 N HYP F 14 1555 1555 1.34 LINK C HYP F 14 N GLY F 15 1555 1555 1.36 CRYST1 25.987 26.668 79.843 90.00 90.03 90.00 P 1 21 1 12 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 0.038481 0.000000 0.000020 0.00000 SCALE2 0.000000 0.037498 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012525 0.00000