HEADER STRUCTURAL PROTEIN 28-SEP-05 2D3H TITLE CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP- TITLE 2 GLY-(PRO-PRO-GLY)4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO- COMPND 3 PRO-GLY)4; COMPND 4 CHAIN: A, B, C, D, E, F; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS COLLAGEN MODEL TRIPLETT WAS CHEMICALLY SOURCE 4 SYSTHESIZED. HYP-HYP-GLY GUEST IN PRO-PRO-GLY HOST PEPTIDE. KEYWDS COLLAGEN, TRIPLE-HELIX, HYDROXYPROLINE, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.WU,K.NOGUCHI,K.OKUYAMA,K.MIZUNO,H.P.BACHINGER REVDAT 4 25-OCT-23 2D3H 1 LINK REVDAT 3 24-MAR-09 2D3H 1 JRNL REVDAT 2 24-FEB-09 2D3H 1 VERSN REVDAT 1 19-SEP-06 2D3H 0 JRNL AUTH K.OKUYAMA,C.HONGO,G.WU,K.MIZUNO,K.NOGUCHI,S.EBISUZAKI, JRNL AUTH 2 Y.TANAKA,N.NISHINO,H.P.BACHINGER JRNL TITL HIGH-RESOLUTION STRUCTURES OF COLLAGEN-LIKE PEPTIDES JRNL TITL 2 [(PRO-PRO-GLY)(4)-XAA-YAA-GLY-(PRO-PRO-GLY)(4)]: JRNL TITL 3 IMPLICATIONS FOR TRIPLE-HELIX HYDRATION AND HYP(X) JRNL TITL 4 PUCKERING. JRNL REF BIOPOLYMERS V. 91 361 2009 JRNL REFN ISSN 0006-3525 JRNL PMID 19137577 JRNL DOI 10.1002/BIP.21138 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)) : 1.000 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) : 0.196 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.193 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1627 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 32044 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.191 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.188 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1431 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 28103 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 895 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 263 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1158.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 823.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10425 REMARK 3 NUMBER OF RESTRAINTS : 12967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.028 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.059 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.047 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.145 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.046 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.076 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. BOTH UP- AND DOWN- REMARK 3 PUCKERINGS WERE OBSERVED FOR PROLINE RING AT THE X POSITION OF REMARK 3 THE GLY-X-Y SEQUENCE. ANISOTROPIC REFINEMENT REDUCED FREE R. REMARK 4 REMARK 4 2D3H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000024940. 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 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 : TRIANGLUALR SI(111) WITH AN REMARK 200 ASYMMETRIC ANGLE OF 7.8 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, HKL-2000 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) : 26.610 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 : 4.5000 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: X-PLOR REMARK 200 STARTING MODEL: PDB 2CUO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1000, ACETATE BUFFER, PH 5.6, 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 13.33400 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 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: 4110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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: 4230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3890 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 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 PRO A 25 REMARK 465 PRO A 26 REMARK 465 GLY A 27 REMARK 465 PRO B 25 REMARK 465 PRO B 26 REMARK 465 GLY B 27 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 GLY E 27 REMARK 465 PRO F 1 REMARK 465 PRO F 2 REMARK 465 GLY F 3 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO C 2 158.30 -49.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CUO RELATED DB: PDB REMARK 900 COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9 REMARK 900 RELATED ID: 1X1K RELATED DB: PDB REMARK 900 HOST-GUEST PEPTIDE (PRO-PRO-GLY)4-(PRO-ALLOHYP-GLY)-(PRO- PRO-GLY)4 REMARK 900 RELATED ID: 1V4F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES WITH PRO-HYP-GLY REMARK 900 SEQUENCE AT 1.3A REMARK 900 RELATED ID: 1V6Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES WITH PRO-HYP-GLY REMARK 900 SEQUENCE AT 1.3A REMARK 900 RELATED ID: 1V7H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES WITH PRO-HYP-GLY REMARK 900 SEQUENCE AT 1.26A REMARK 900 RELATED ID: 1YM8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF GZZ SHOWS UP PUCKERING OF THE PROLINE RING IN REMARK 900 THE XAA POSITION REMARK 900 RELATED ID: 2D3F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-PRO- REMARK 900 HYP-GLY-(PRO-PRO-GLY)4 DBREF 2D3H A 1 27 PDB 2D3H 2D3H 1 27 DBREF 2D3H B 1 27 PDB 2D3H 2D3H 1 27 DBREF 2D3H C 1 27 PDB 2D3H 2D3H 1 27 DBREF 2D3H D 1 27 PDB 2D3H 2D3H 1 27 DBREF 2D3H E 1 27 PDB 2D3H 2D3H 1 27 DBREF 2D3H F 1 27 PDB 2D3H 2D3H 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 2D3H HYP A 13 PRO 4-HYDROXYPROLINE MODRES 2D3H HYP A 14 PRO 4-HYDROXYPROLINE MODRES 2D3H HYP B 13 PRO 4-HYDROXYPROLINE MODRES 2D3H HYP B 14 PRO 4-HYDROXYPROLINE MODRES 2D3H HYP C 13 PRO 4-HYDROXYPROLINE MODRES 2D3H HYP C 14 PRO 4-HYDROXYPROLINE MODRES 2D3H HYP D 13 PRO 4-HYDROXYPROLINE MODRES 2D3H HYP D 14 PRO 4-HYDROXYPROLINE MODRES 2D3H HYP E 13 PRO 4-HYDROXYPROLINE MODRES 2D3H HYP E 14 PRO 4-HYDROXYPROLINE MODRES 2D3H HYP F 13 PRO 4-HYDROXYPROLINE MODRES 2D3H 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 *263(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 1.33 LINK C HYP A 14 N GLY A 15 1555 1555 1.33 LINK C GLY B 12 N HYP B 13 1555 1555 1.34 LINK C HYP B 13 N HYP B 14 1555 1555 1.31 LINK C HYP B 14 N GLY B 15 1555 1555 1.31 LINK C GLY C 12 N HYP C 13 1555 1555 1.32 LINK C HYP C 13 N HYP C 14 1555 1555 1.31 LINK C HYP C 14 N GLY C 15 1555 1555 1.33 LINK C GLY D 12 N HYP D 13 1555 1555 1.35 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 1.33 LINK C HYP E 13 N HYP E 14 1555 1555 1.31 LINK C HYP E 14 N GLY E 15 1555 1555 1.33 LINK C GLY F 12 N HYP F 13 1555 1555 1.30 LINK C HYP F 13 N HYP F 14 1555 1555 1.32 LINK C HYP F 14 N GLY F 15 1555 1555 1.33 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