10 20 30 40 50 60 70 80 1X1K - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL PROTEIN 05-APR-05 1X1K
TITLE HOST-GUEST PEPTIDE (PRO-PRO-GLY)4-(PRO-ALLOHYP-GLY)-(PRO- TITLE 2 PRO-GLY)4
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HOST-GUEST PEPTIDE (PRO-PRO-GLY)4-(PRO-ALLOHYP- COMPND 3 GLY)-(PRO-PRO-GLY)4; COMPND 4 CHAIN: A, B, C, D, E; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HOST-GUEST PEPTIDE (PRO-PRO-GLY)4-(PRO-ALLOHYP- COMPND 8 GLY)-(PRO-PRO-GLY)4; COMPND 9 CHAIN: F; COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: COLLAGEN MODEL PEPTIDE WAS CHEMICALLY SOURCE 4 SYSTHESIZED; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: COLLAGEN MODEL PEPTIDE WAS CHEMICALLY SOURCE 8 SYSTHESIZED
KEYWDS ALLO-HYP, NON-NATURAL AMINO ACID, COLLAGEN MODEL PEPTIDE, KEYWDS 2 PUCKERING, TRIPLE-HELIX STABILITY, STRUCTURAL PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR N.JIRAVANICHANUN,C.HONGO,G.WU,K.NOGUCHI,K.OKUYAMA,N.NISHINO, AUTHOR 2 T.SILVA
REVDAT 3 24-FEB-09 1X1K 1 VERSN REVDAT 2 13-SEP-05 1X1K 1 JRNL REVDAT 1 14-JUN-05 1X1K 0
JRNL AUTH N.JIRAVANICHANUN,C.HONGO,G.WU,K.NOGUCHI,K.OKUYAMA, JRNL AUTH 2 N.NISHINO,T.SILVA JRNL TITL UNEXPECTED PUCKERING OF HYDROXYPROLINE IN THE JRNL TITL 2 GUEST TRIPLETS, HYP-PRO-GLY AND PRO-ALLOHYP-GLY JRNL TITL 3 SANDWICHED BETWEEN PRO-PRO-GLY SEQUENCE JRNL REF CHEMBIOCHEM V. 6 1184 2005 JRNL REFN ISSN 1439-4227 JRNL PMID 15929160 JRNL DOI 10.1002/CBIC.200500055
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH N.JIRAVANICHANUN,K.NOGUCHI,K.OKUYAMA,N.NISHINO REMARK 1 TITL HIGH RESOLUTION STRUCTURE OF COLLAGEN MODEL REMARK 1 TITL 2 PEPTIDE SEQUENCE REMARK 1 TITL 3 (PRO-PRO-GLY)4-(PRO-ALLOHYP-GLY)-(PRO-PRO-GLY)4 REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN
REMARK 2 REMARK 2 RESOLUTION. 1.10 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.3 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) : 0.173 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2149 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 41288 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.158 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)) : 31246 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 992 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 284 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1258.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 855.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 1 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 11488 REMARK 3 NUMBER OF RESTRAINTS : 15246 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.013 REMARK 3 ANGLE DISTANCES (A) : 0.027 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.039 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.071 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.059 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.010 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.030 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.086 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: NULL
REMARK 4 REMARK 4 1X1K COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-APR-05. REMARK 100 THE RCSB ID CODE IS RCSB024262.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 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) : 0.8, 1 REMARK 200 MONOCHROMATOR : SILICON REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43437 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: PDB ENTRY 1ITT REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 29.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG200, PH 7, VAPOR DIFFUSION, REMARK 280 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 13.01950 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10050 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -75.0 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 E 27 REMARK 465 GLY F 30
REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO C 1 PRO C 2 124.16 REMARK 500 REMARK 500 REMARK: NULL
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 C2099 DISTANCE = 5.28 ANGSTROMS
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ITT RELATED DB: PDB REMARK 900 (PRO-PRO-GLY)9
DBREF 1X1K A 1 27 PDB 1X1K 1X1K 1 27 DBREF 1X1K B 1 27 PDB 1X1K 1X1K 1 27 DBREF 1X1K C 1 27 PDB 1X1K 1X1K 1 27 DBREF 1X1K D 1 27 PDB 1X1K 1X1K 1 27 DBREF 1X1K E 1 27 PDB 1X1K 1X1K 1 27 DBREF 1X1K F 1 30 PDB 1X1K 1X1K 1 30
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 30 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO SEQRES 2 F 30 HYP GLY PRO HYP GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 F 30 GLY PRO PRO GLY
MODRES 1X1K HYP A 14 PRO 4-HYDROXYPROLINE MODRES 1X1K HYP B 14 PRO 4-HYDROXYPROLINE MODRES 1X1K HYP C 14 PRO 4-HYDROXYPROLINE MODRES 1X1K HYP D 14 PRO 4-HYDROXYPROLINE MODRES 1X1K HYP E 14 PRO 4-HYDROXYPROLINE MODRES 1X1K HYP F 14 PRO 4-HYDROXYPROLINE MODRES 1X1K HYP F 17 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 HET HYP F 17 8
HETNAM HYP 4-HYDROXYPROLINE
HETSYN HYP HYDROXYPROLINE
FORMUL 1 HYP 7(C5 H9 N O3) FORMUL 7 HOH *283(H2 O)
LINK C PRO A 13 N HYP A 14 1555 1555 1.33 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 1.36 LINK C PRO C 13 N HYP C 14 1555 1555 1.33 LINK C HYP C 14 N GLY C 15 1555 1555 1.31 LINK C PRO D 13 N HYP D 14 1555 1555 1.32 LINK C HYP D 14 N GLY D 15 1555 1555 1.31 LINK C PRO E 13 N HYP E 14 1555 1555 1.32 LINK C HYP E 14 N GLY E 15 1555 1555 1.32 LINK C PRO F 13 N HYP F 14 1555 1555 1.31 LINK C HYP F 14 N GLY F 15 1555 1555 1.34 LINK C PRO F 16 N HYP F 17 1555 1555 1.33 LINK C HYP F 17 N GLY F 18 1555 1555 1.34
CRYST1 26.445 26.039 80.309 90.00 89.98 90.00 P 1 21 1 10
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 0.037814 0.000000 -0.000013 0.00000
SCALE2 0.000000 0.038404 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012452 0.00000