HEADER STRUCTURAL PROTEIN 03-APR-09 3A1H TITLE CRYSTAL STRUCTURE ANALYSIS OF THE COLLAGEN-LIKE PEPTIDE, (PPG)4-OTG- TITLE 2 (PPG)4 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 HELIX, HOST-GUEST PEPTIDE, TWINNED CRYSTAL, STRUCTURAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.OKUYAMA,K.MIYAMA,K.MIZUNO,H.P.BACHINGER REVDAT 3 01-NOV-23 3A1H 1 LINK REVDAT 2 27-JUL-11 3A1H 1 JRNL REMARK REVDAT 1 23-MAR-10 3A1H 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. 1.08 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) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 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) : 0.135 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2279 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 45529 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)) : 0.134 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)) : 42563 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 864 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 222 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1086.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 9778 REMARK 3 NUMBER OF RESTRAINTS : 12276 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.034 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.037 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.095 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.073 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.012 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.007 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.061 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.085 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 TWINNING FRACTION 0.44 USING THE REMARK 3 TWINNED DATA. REMARK 4 REMARK 4 3A1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-APR-09. REMARK 100 THE DEPOSITION ID IS D_1000028692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU 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 : THE ROTATED-INCLINED DOUBLE REMARK 200 CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46090 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.080 REMARK 200 RESOLUTION RANGE LOW (A) : 26.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.260 REMARK 200 R MERGE (I) : 0.07600 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) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.33 REMARK 200 R MERGE FOR SHELL (I) : 0.30400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.900 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: 2CUO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5%(W/V) PEG 400, 0.1M MES BUFFER, REMARK 280 PH 5.9, VAPOR DIFFUSION, SITTING 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 13.24500 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: 4090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3830 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: 4030 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3790 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 1 REMARK 465 PRO A 2 REMARK 465 PRO A 26 REMARK 465 GLY A 27 REMARK 465 PRO B 26 REMARK 465 GLY B 27 REMARK 465 PRO C 1 REMARK 465 PRO C 2 REMARK 465 GLY C 27 REMARK 465 PRO D 1 REMARK 465 PRO D 2 REMARK 465 GLY D 27 REMARK 465 PRO E 1 REMARK 465 PRO E 2 REMARK 465 GLY E 27 REMARK 465 PRO F 1 REMARK 465 PRO F 2 REMARK 465 GLY F 3 REMARK 465 PRO F 4 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO F 16 C - N - CA ANGL. DEV. = 10.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CUO RELATED DB: PDB REMARK 900 THE SIMILAR COLLAGEN-LIKE PEPTIDE REMARK 900 RELATED ID: 3A19 RELATED DB: PDB REMARK 900 THE SIMILAR HOST-GUEST PEPTIDE REMARK 900 RELATED ID: 3A0M 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: 3A08 RELATED DB: PDB REMARK 900 THE SIMILAR HOST-GUEST PEPTIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS SEQUENCE ADOPTS A TRIPLE-HELICAL STRUCURE SIMILAR TO THE REMARK 999 COLLAGEN-HELIX. DBREF 3A1H A 1 27 PDB 3A1H 3A1H 1 27 DBREF 3A1H B 1 27 PDB 3A1H 3A1H 1 27 DBREF 3A1H C 1 27 PDB 3A1H 3A1H 1 27 DBREF 3A1H D 1 27 PDB 3A1H 3A1H 1 27 DBREF 3A1H E 1 27 PDB 3A1H 3A1H 1 27 DBREF 3A1H F 1 27 PDB 3A1H 3A1H 1 27 SEQRES 1 A 27 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY HYP SEQRES 2 A 27 THR 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 THR 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 THR 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 THR 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 THR 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 THR GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 F 27 GLY MODRES 3A1H HYP A 13 PRO 4-HYDROXYPROLINE MODRES 3A1H HYP B 13 PRO 4-HYDROXYPROLINE MODRES 3A1H HYP C 13 PRO 4-HYDROXYPROLINE MODRES 3A1H HYP D 13 PRO 4-HYDROXYPROLINE MODRES 3A1H HYP E 13 PRO 4-HYDROXYPROLINE MODRES 3A1H HYP F 13 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 HETNAM HYP 4-HYDROXYPROLINE HETSYN HYP HYDROXYPROLINE FORMUL 1 HYP 6(C5 H9 N O3) FORMUL 7 HOH *222(H2 O) LINK C GLY A 12 N HYP A 13 1555 1555 1.31 LINK C HYP A 13 N THR A 14 1555 1555 1.33 LINK C GLY B 12 N HYP B 13 1555 1555 1.36 LINK C HYP B 13 N THR B 14 1555 1555 1.30 LINK C GLY C 12 N HYP C 13 1555 1555 1.33 LINK C HYP C 13 N THR C 14 1555 1555 1.34 LINK C GLY D 12 N HYP D 13 1555 1555 1.34 LINK C HYP D 13 N THR D 14 1555 1555 1.31 LINK C GLY E 12 N HYP E 13 1555 1555 1.31 LINK C HYP E 13 N THR E 14 1555 1555 1.33 LINK C GLY F 12 N HYP F 13 1555 1555 1.31 LINK C HYP F 13 N THR F 14 1555 1555 1.34 CRYST1 25.990 26.490 80.210 90.00 89.85 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 0.038476 0.000000 -0.000101 0.00000 SCALE2 0.000000 0.037750 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012467 0.00000