10 20 30 40 50 60 70 80 2D3F - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL PROTEIN 27-SEP-05 2D3F
TITLE CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY) TITLE 2 4-PRO-HYP-GLY-(PRO-PRO-GLY)4
COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-PRO-HYP- COMPND 3 GLY-(PRO-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: COLLAGEN MODEL PEPTIDE WAS CHEMICALLY SOURCE 4 SYSTHESIZED. PRO-HYP-GLY GUEST IN PRO-PRO-GLY HOST PEPTIDE.
KEYWDS COLLAGEN, CRYSTAL STRUCTURE, TRIPLE-HELIX, HYDROXYPROLINE, KEYWDS 2 STRUCTURAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR G.WU,K.NOGUCHI,K.OKUYAMA,S.EBISUZAKI,N.NISHINO
REVDAT 3 24-MAR-09 2D3F 1 JRNL REVDAT 2 24-FEB-09 2D3F 1 VERSN REVDAT 1 19-SEP-06 2D3F 0
JRNL AUTH K.OKUYAMA,C.HONGO,G.WU,K.MIZUNO,K.NOGUCHI, JRNL AUTH 2 S.EBISUZAKI,Y.TANAKA,N.NISHINO,H.P.BACHINGER JRNL TITL HIGH-RESOLUTION STRUCTURES OF COLLAGEN-LIKE JRNL TITL 2 PEPTIDES [(PRO-PRO-GLY)(4)-XAA-YAA-GLY-(PRO-PRO- JRNL TITL 3 GLY)(4)]: IMPLICATIONS FOR TRIPLE-HELIX HYDRATION JRNL TITL 4 AND HYP(X) PUCKERING. JRNL REF BIOPOLYMERS V. 91 361 2009 JRNL REFN ISSN 0006-3525 JRNL PMID 19137577 JRNL DOI 10.1002/BIP.21138
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.26 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) : 1.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 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) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL 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)) : 0.185 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.183 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 1122 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 22440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 968 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 304 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1272.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 909.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 9908 REMARK 3 NUMBER OF RESTRAINTS : 12445 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.022 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) : 0.046 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.042 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.131 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.003 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.048 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.040 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 REMARK 3 GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE REMARK 3 (0 0 1) TRANSLATION USING FRACTIONAL COORDINATES. BOTH UP- AND REMARK 3 DOWN- PUCKERINGS WERE OBSERVED FOR PROLINE RING AT THE X REMARK 3 POSITION OF THE GLY-X-Y SEQUENCE. ANISOTROPIC REFINEMENT REMARK 3 REDUCED FREE R.
REMARK 4 REMARK 4 2D3F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-SEP-05. REMARK 100 THE RCSB ID CODE IS RCSB024938.
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 : NULL 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26765 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.260 REMARK 200 RESOLUTION RANGE LOW (A) : 26.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.3 REMARK 200 DATA REDUNDANCY : 6.870 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.41 REMARK 200 R MERGE FOR SHELL (I) : 0.33100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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 (%): 27.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 400, VAPOR DIFFUSION, HANGING REMARK 280 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 13.26600 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: 4310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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: 4480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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: 9720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -70.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, 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 27 REMARK 465 GLY B 27 REMARK 465 GLY C 27
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH E1223 DISTANCE = 5.69 ANGSTROMS REMARK 525 HOH D1283 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH E1280 DISTANCE = 9.59 ANGSTROMS REMARK 525 HOH D1291 DISTANCE = 5.06 ANGSTROMS REMARK 525 HOH A1269 DISTANCE = 5.42 ANGSTROMS REMARK 525 HOH A1287 DISTANCE = 7.92 ANGSTROMS
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- REMARK 900 PRO-GLY)4 REMARK 900 RELATED ID: 1V4F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES WITH PRO-HYP- REMARK 900 GLY SEQUENCE AT 1.3A REMARK 900 RELATED ID: 1V6Q RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES WITH PRO-HYP- REMARK 900 GLY SEQUENCE AT 1.3A REMARK 900 RELATED ID: 1V7H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES WITH PRO-HYP- REMARK 900 GLY SEQUENCE AT 1.26A REMARK 900 RELATED ID: 2D3H RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY) REMARK 900 4-HYP-HYP-GLY-(PRO-PRO-GLY)4
DBREF 2D3F A 1 27 PDB 2D3F 2D3F 1 27 DBREF 2D3F B 1 27 PDB 2D3F 2D3F 1 27 DBREF 2D3F C 1 27 PDB 2D3F 2D3F 1 27 DBREF 2D3F D 1 27 PDB 2D3F 2D3F 1 27 DBREF 2D3F E 1 27 PDB 2D3F 2D3F 1 27 DBREF 2D3F F 1 27 PDB 2D3F 2D3F 1 27
SEQRES 1 A 27 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO 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 PRO 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 PRO 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 PRO 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 PRO 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 PRO SEQRES 2 F 27 HYP GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 F 27 GLY
MODRES 2D3F HYP A 14 PRO 4-HYDROXYPROLINE MODRES 2D3F HYP B 14 PRO 4-HYDROXYPROLINE MODRES 2D3F HYP C 14 PRO 4-HYDROXYPROLINE MODRES 2D3F HYP D 14 PRO 4-HYDROXYPROLINE MODRES 2D3F HYP E 14 PRO 4-HYDROXYPROLINE MODRES 2D3F HYP F 14 PRO 4-HYDROXYPROLINE
HET HYP A 14 8 HET HYP B 14 8 HET HYP C 14 8 HET HYP D 14 8 HET HYP E 14 8 HET HYP F 14 8
HETNAM HYP 4-HYDROXYPROLINE
HETSYN HYP HYDROXYPROLINE
FORMUL 1 HYP 6(C5 H9 N O3) FORMUL 7 HOH *304(H2 O)
LINK C PRO A 13 N HYP A 14 1555 1555 1.32 LINK C HYP A 14 N GLY A 15 1555 1555 1.31 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 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 PRO D 13 N HYP D 14 1555 1555 1.33 LINK C HYP D 14 N GLY D 15 1555 1555 1.35 LINK C PRO E 13 N HYP E 14 1555 1555 1.33 LINK C HYP E 14 N GLY E 15 1555 1555 1.32 LINK C PRO F 13 N HYP F 14 1555 1555 1.32 LINK C HYP F 14 N GLY F 15 1555 1555 1.33
CRYST1 26.082 26.532 79.843 90.00 89.97 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 0.038341 0.000000 -0.000020 0.00000
SCALE2 0.000000 0.037690 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012525 0.00000