HEADER STRUCTURAL PROTEIN 21-MAR-09 3A0M TITLE STRUCTURE OF (PPG)4-OVG-(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, TRIPLE-HELIX, MODEL PEPTIDE, TWINNED CRYSTAL, STRUCTURAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.OKUYAMA,T.MORIMOTO,K.MIZUNO,H.P.BACHINGER REVDAT 3 06-JUN-12 3A0M 1 SEQADV REVDAT 2 27-JUL-11 3A0M 1 JRNL REMARK REVDAT 1 02-MAR-10 3A0M 0 JRNL AUTH K.OKUYAMA,K.MIYAMA,T.MORIMOTO,K.MASAKIYO,K.MIZUNO, JRNL AUTH 2 H.P.BACHINGER JRNL TITL STABILIZATION OF TRIPLE-HELICAL STRUCTURES OF COLLAGEN JRNL TITL 2 PEPTIDES CONTAINING A HYP-THR-GLY, HYP-VAL-GLY, OR JRNL TITL 3 HYP-SER-GLY SEQUENCE. JRNL REF BIOPOLYMERS V. 95 628 2011 JRNL REFN ISSN 0006-3525 JRNL PMID 21442606 JRNL DOI 10.1002/BIP.21625 REMARK 2 REMARK 2 RESOLUTION. 1.02 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) : 1.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.1 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) : 0.116 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2698 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)) : 0.108 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)) : 46193 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 925 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 280 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1173.61 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 847.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 10 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10851 REMARK 3 NUMBER OF RESTRAINTS : 13920 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.032 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.087 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.064 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.017 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.043 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.087 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 REFINED UNDER THE REMARK 3 TWINNING OPERATOR (H,-K,-L) AND THE TWINNING FRACTION 0.395 USING REMARK 3 THE TWINNED DATA. REMARK 4 REMARK 4 3A0M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAR-09. REMARK 100 THE RCSB ID CODE IS RCSB028661. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.70 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : DOUBLE-CRYSTAL MONOCHROMATOR & REMARK 200 HORIZONTAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : BRUKER DIP-6040 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60025 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.980 REMARK 200 RESOLUTION RANGE LOW (A) : 24.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.05000 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) : 0.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: PDB ENTRY 2CUO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 11.3%(W/V) PEG 2000, 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 13.18300 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: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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: 4160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -29.0 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 GLY A 27 REMARK 465 PRO B 1 REMARK 465 PRO B 2 REMARK 465 GLY B 3 REMARK 465 PRO C 1 REMARK 465 PRO C 2 REMARK 465 PRO D 1 REMARK 465 PRO D 2 REMARK 465 GLY D 27 REMARK 465 PRO E 26 REMARK 465 GLY E 27 REMARK 465 PRO F 1 REMARK 465 PRO F 2 REMARK 465 GLY F 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PRO F 16 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A08 RELATED DB: PDB REMARK 900 THE SIMILAR HOST-GUEST PEPTIDE REMARK 900 RELATED ID: 3A0A RELATED DB: PDB REMARK 900 THE SIMILAR HOST-GUEST PEPTIDE REMARK 900 RELATED ID: 2CUO RELATED DB: PDB REMARK 900 THE SIMILAR COLLAGEN-LIKE PEPTIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS SEQUENCE ADOPTS A TRIPLE-HELICAL STRUCTURE SIMILAR TO THE REMARK 999 COLLAGEN-HELIX. THE RESIDUES PRO F 13, PRO F 14, HYP F 16, VAL F 17 REMARK 999 ASSIGNED ALTERNATE POSITION B ARE MICROHETEROGENEITY. DBREF 3A0M A 1 27 PDB 3A0M 3A0M 1 27 DBREF 3A0M B 1 27 PDB 3A0M 3A0M 1 27 DBREF 3A0M C 1 27 PDB 3A0M 3A0M 1 27 DBREF 3A0M D 1 27 PDB 3A0M 3A0M 1 27 DBREF 3A0M E 1 27 PDB 3A0M 3A0M 1 27 DBREF 3A0M F 1 27 PDB 3A0M 3A0M 1 27 SEQADV 3A0M PRO F 13 PDB 3A0M HYP 13 MICROHETEROGENEITY SEQADV 3A0M PRO F 14 PDB 3A0M VAL 14 MICROHETEROGENEITY SEQADV 3A0M HYP F 16 PDB 3A0M PRO 16 MICROHETEROGENEITY SEQADV 3A0M VAL F 17 PDB 3A0M PRO 17 MICROHETEROGENEITY SEQRES 1 A 27 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY HYP SEQRES 2 A 27 VAL 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 VAL 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 VAL 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 VAL 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 VAL 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 VAL GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 F 27 GLY MODRES 3A0M HYP A 13 PRO 4-HYDROXYPROLINE MODRES 3A0M HYP B 13 PRO 4-HYDROXYPROLINE MODRES 3A0M HYP C 13 PRO 4-HYDROXYPROLINE MODRES 3A0M HYP D 13 PRO 4-HYDROXYPROLINE MODRES 3A0M HYP E 13 PRO 4-HYDROXYPROLINE MODRES 3A0M HYP F 13 PRO 4-HYDROXYPROLINE MODRES 3A0M HYP F 16 PRO 4-HYDROXYPROLINE HET HYP A 13 8 HET HYP B 13 8 HET HYP C 13 8 HET HYP D 13 8 HET HYP E 13 8 HET HYP F 13 8 HET HYP F 16 8 HETNAM HYP 4-HYDROXYPROLINE HETSYN HYP HYDROXYPROLINE FORMUL 1 HYP 7(C5 H9 N O3) FORMUL 7 HOH *280(H2 O) LINK C GLY A 12 N HYP A 13 1555 1555 1.35 LINK C HYP A 13 N VAL A 14 1555 1555 1.35 LINK C GLY B 12 N HYP B 13 1555 1555 1.33 LINK C HYP B 13 N VAL B 14 1555 1555 1.33 LINK C GLY C 12 N HYP C 13 1555 1555 1.34 LINK C HYP C 13 N VAL C 14 1555 1555 1.33 LINK C GLY D 12 N HYP D 13 1555 1555 1.35 LINK C HYP D 13 N VAL D 14 1555 1555 1.34 LINK C GLY E 12 N HYP E 13 1555 1555 1.35 LINK C HYP E 13 N VAL E 14 1555 1555 1.32 LINK C GLY F 12 N AHYP F 13 1555 1555 1.33 LINK C AHYP F 13 N AVAL F 14 1555 1555 1.31 LINK C BGLY F 15 N BHYP F 16 1555 1555 1.34 LINK C BHYP F 16 N BVAL F 17 1555 1555 1.31 SITE 1 AC1 10 GLY D 15 VAL E 14 GLY E 15 GLY F 15 SITE 2 AC1 10 PRO F 16 PRO F 17 GLY F 18 HOH F 266 SITE 3 AC1 10 HOH F 339 HOH F 353 CRYST1 26.124 26.366 79.939 90.00 90.08 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 0.038279 0.000000 0.000053 0.00000 SCALE2 0.000000 0.037928 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012510 0.00000 MASTER 226 0 7 0 0 0 3 6 0 0 0 18 END