HEADER STRUCTURAL PROTEIN 13-NOV-03 1V4F TITLE CRYSTAL STRUCTURES OF COLLAGEN MODEL PEPTIDES WITH PRO-HYP-GLY TITLE 2 SEQUENCE AT 1.3A 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: THIS TRIPLET IS VERY POPULAR IN THE COLLAGEN SOURCE 4 SEQUENCE.; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: THIS TRIPLET IS VERY POPULAR IN THE COLLAGEN SOURCE 8 SEQUENCE.; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES; SOURCE 11 OTHER_DETAILS: THIS TRIPLET IS VERY POPULAR IN THE COLLAGEN SOURCE 12 SEQUENCE. KEYWDS COLLAGEN, TRIPLE-HELIX, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.OKUYAMA,C.HONGO,R.FUKUSHIMA,G.WU,K.NOGUCHI,Y.TANAKA,N.NISHINO REVDAT 4 25-DEC-13 1V4F 1 REMARK VERSN REVDAT 3 24-FEB-09 1V4F 1 VERSN REVDAT 2 21-DEC-04 1V4F 1 JRNL REVDAT 1 03-AUG-04 1V4F 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. 1.26 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) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 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) : 0.133 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 176 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 3520 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)) : 0.132 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.157 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 170 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 3395 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 : 49 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 182.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 112.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1396 REMARK 3 NUMBER OF RESTRAINTS : 1698 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.055 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.034 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.080 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.059 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.011 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.035 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. BOTH UP- AND DOWN- REMARK 3 PUCKERINGS WERE OBSERVED FOR PROLINE RING AT THE X POSITION OF REMARK 3 THE GLY-X-Y SEQUENCE. REMARK 4 REMARK 4 1V4F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-NOV-03. REMARK 100 THE RCSB ID CODE IS RCSB006192. 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) : 100 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) : 1.0 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 : 3520 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.260 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 6.670 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.03500 REMARK 200 FOR THE DATA SET : 3.3000 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) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.66 REMARK 200 R MERGE FOR SHELL (I) : 0.19000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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: (PRO-HYP-GLY)10 STRUCTURE REPORTED IN V.NAGARAJAN, REMARK 200 S.KAMITORI, K.OKUYAMA, J.BIOCHEM. 125, 310 (1999) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 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 13.09050 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 2 - 7 BY (001), AND REMARK 300 RESIDUES 1-7 BY (002), (003), (004), (005). REMARK 300 CHAIN B: TRANSLATE RESIDUES 3 - 7 BY (001), AND REMARK 300 RESIDUES 1-7 BY (002), (003), (004) AND REMARK 300 RESIDUE 1-5 BY (005). REMARK 300 CHAIN C: TRANSLATE RESIDUES 1 - 7 BY (001), (002), REMARK 300 (003) (004), AND RESIDUES 1-6 BY (005). 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: TRIMERIC 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 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 7 N PRO C 1 1556 1.33 REMARK 500 N GLY A 1 C HYP B 7 1554 1.34 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 B 15 DISTANCE = 5.09 ANGSTROMS REMARK 525 HOH B 29 DISTANCE = 8.01 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CAG RELATED DB: PDB REMARK 900 SIMILAR SEQUENCE REMARK 900 RELATED ID: 1V6Q RELATED DB: PDB REMARK 900 THE SAME PEPTIDE MEASURED AT RT REMARK 900 RELATED ID: 1V7H RELATED DB: PDB REMARK 900 HOLOMOLOGOUS PEPTIDE MEASURED AT 100K DBREF 1V4F A 1 7 PDB 1V4F 1V4F 1 7 DBREF 1V4F B 1 7 PDB 1V4F 1V4F 1 7 DBREF 1V4F C 1 7 PDB 1V4F 1V4F 1 7 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 1V4F HYP A 3 PRO 4-HYDROXYPROLINE MODRES 1V4F HYP A 6 PRO 4-HYDROXYPROLINE MODRES 1V4F HYP B 1 PRO 4-HYDROXYPROLINE MODRES 1V4F HYP B 4 PRO 4-HYDROXYPROLINE MODRES 1V4F HYP B 7 PRO 4-HYDROXYPROLINE MODRES 1V4F HYP C 2 PRO 4-HYDROXYPROLINE MODRES 1V4F HYP C 5 PRO 4-HYDROXYPROLINE HET HYP A 3 8 HET HYP A 6 8 HET HYP B 1 8 HET HYP B 4 8 HET HYP B 7 8 HET HYP C 2 8 HET HYP C 5 8 HETNAM HYP 4-HYDROXYPROLINE HETSYN HYP HYDROXYPROLINE FORMUL 1 HYP 7(C5 H9 N O3) FORMUL 4 HOH *49(H2 O) LINK C PRO A 2 N HYP A 3 1555 1555 1.32 LINK C HYP A 3 N GLY A 4 1555 1555 1.33 LINK C PRO A 5 N HYP A 6 1555 1555 1.33 LINK C HYP A 6 N GLY A 7 1555 1555 1.33 LINK C HYP B 1 N GLY B 2 1555 1555 1.32 LINK C PRO B 3 N HYP B 4 1555 1555 1.33 LINK C HYP B 4 N GLY B 5 1555 1555 1.33 LINK C PRO B 6 N HYP B 7 1555 1555 1.31 LINK C PRO C 1 N HYP C 2 1555 1555 1.33 LINK C HYP C 2 N GLY C 3 1555 1555 1.33 LINK C PRO C 4 N HYP C 5 1555 1555 1.33 LINK C HYP C 5 N GLY C 6 1555 1555 1.33 LINK C HYP B 7 N GLY A 1 1555 1556 1.34 LINK C PRO C 7 N HYP B 1 1554 1555 1.33 CRYST1 13.864 26.181 19.877 90.00 105.75 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 0.072129 0.000000 0.020343 0.00000 SCALE2 0.000000 0.038196 0.000000 0.00000 SCALE3 0.000000 0.000000 0.052272 0.00000 MASTER 227 0 7 0 0 0 0 6 0 0 0 3 END