HEADER STRUCTURAL PROTEIN 22-JAN-10 3ADM TITLE CRYSTAL STRUCTURE OF (PRO-PRO-GLY)4-HYP-SER-GLY-(PRO-PRO-GLY)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, TRIPLE HELIX, MODEL PEPTIDE, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.OKUYAMA,K.MIYAMA,K.MASAKIYO,K.MIZUNO,H.P.BACHINGER REVDAT 2 27-JUL-11 3ADM 1 JRNL REVDAT 1 19-JAN-11 3ADM 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. 1.18 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) : 1.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.6 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) : 0.166 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1745 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)) : 0.149 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)) : 25946 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 963 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 : 1229.35 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 846.90 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 16 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 11326 REMARK 3 NUMBER OF RESTRAINTS : 15805 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 ANGLE DISTANCES (A) : 0.024 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.031 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.065 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.048 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.009 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.042 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: NULL REMARK 4 REMARK 4 3ADM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-FEB-10. REMARK 100 THE RCSB ID CODE IS RCSB029120. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 100 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) : 0.9 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR 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 : 34897 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.180 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.1 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.04600 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) : 1.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.31300 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 (%): 38.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 11.3% PEG 2000, 0.05M ACETATE BUFFER, REMARK 280 PH 5.6, 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 13.05100 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: 4440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4270 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: 4270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 3940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, F, E 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 C 1 REMARK 465 GLY D 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 A 341 DISTANCE = 5.15 ANGSTROMS REMARK 525 HOH B 274 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH B 364 DISTANCE = 6.82 ANGSTROMS REMARK 525 HOH B 374 DISTANCE = 5.49 ANGSTROMS REMARK 525 HOH B 379 DISTANCE = 5.64 ANGSTROMS REMARK 525 HOH B 380 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH C 368 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH D 315 DISTANCE = 5.42 ANGSTROMS REMARK 525 HOH D 369 DISTANCE = 5.13 ANGSTROMS REMARK 525 HOH E 334 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH F 295 DISTANCE = 5.10 ANGSTROMS REMARK 525 HOH F 332 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH F 361 DISTANCE = 6.60 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3A1H 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: 3A08 RELATED DB: PDB REMARK 900 THE SIMILAR HOST-GUEST PEPTIDE REMARK 900 RELATED ID: 3A19 RELATED DB: PDB REMARK 900 THE SIMILAR HOST-GUEST PEPTIDE REMARK 900 RELATED ID: 3ABN 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 999 REMARK 999 SEQUENCE REMARK 999 THIS SEQUENCE ADOPTS COLLAGEN-HELIX. THE AUTHOR STATES THAT CHAIN E REMARK 999 HAS A DISORDERED STRUCTURE IN THE CENTRAL REGION. THE AUTHOR FOUND REMARK 999 HYP AND SER IN TWO POSITIONS. THEREFORE THEY PRETENDED THAT THE E- REMARK 999 CHAIN CONSISTS OF TWO CHAINS WITH DIFFERENT OCCUPANCIES. THESE TWO REMARK 999 CHAINS ARE ASSIGNED WITH ALTERNATE POSITION A AND B AND HAVE REMARK 999 EXACTLY THE SAME ATOMIC COORDINATES PARTIALLY. PRO_4 - GLY_12 (ALT. REMARK 999 A) AND PRO_1 - GLY_9 (ALT. B) ARE SAME. GLY_18 - GLY_27 (ALT. A) REMARK 999 AND GLY_15 - GLY_24 (ALT. B) ARE SAME. DBREF 3ADM A 1 27 PDB 3ADM 3ADM 1 27 DBREF 3ADM B 1 27 PDB 3ADM 3ADM 1 27 DBREF 3ADM C 1 27 PDB 3ADM 3ADM 1 27 DBREF 3ADM D 1 27 PDB 3ADM 3ADM 1 27 DBREF 3ADM E 1 27 PDB 3ADM 3ADM 1 27 DBREF 3ADM F 1 27 PDB 3ADM 3ADM 1 27 SEQRES 1 A 27 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY HYP SEQRES 2 A 27 SER 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 SER 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 SER 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 SER 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 SER 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 SER GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 F 27 GLY MODRES 3ADM HYP A 13 PRO 4-HYDROXYPROLINE MODRES 3ADM HYP B 13 PRO 4-HYDROXYPROLINE MODRES 3ADM HYP C 13 PRO 4-HYDROXYPROLINE MODRES 3ADM HYP D 13 PRO 4-HYDROXYPROLINE MODRES 3ADM HYP E 13 PRO 4-HYDROXYPROLINE MODRES 3ADM 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 16 HET HYP F 13 8 HETNAM HYP 4-HYDROXYPROLINE HETSYN HYP HYDROXYPROLINE FORMUL 1 HYP 6(C5 H9 N O3) FORMUL 7 HOH *280(H2 O) LINK C GLY A 12 N HYP A 13 1555 1555 1.33 LINK C HYP A 13 N SER A 14 1555 1555 1.35 LINK C GLY B 12 N HYP B 13 1555 1555 1.34 LINK C HYP B 13 N ASER B 14 1555 1555 1.33 LINK C HYP B 13 N BSER B 14 1555 1555 1.32 LINK C GLY C 12 N HYP C 13 1555 1555 1.34 LINK C HYP C 13 N SER C 14 1555 1555 1.30 LINK C GLY D 12 N HYP D 13 1555 1555 1.34 LINK C HYP D 13 N SER D 14 1555 1555 1.32 LINK C AGLY E 12 N AHYP E 13 1555 1555 1.33 LINK C BGLY E 12 N BHYP E 13 1555 1555 1.33 LINK C AHYP E 13 N ASER E 14 1555 1555 1.33 LINK C BHYP E 13 N BSER E 14 1555 1555 1.33 LINK C GLY F 12 N HYP F 13 1555 1555 1.33 LINK C HYP F 13 N SER F 14 1555 1555 1.31 CRYST1 26.520 26.102 79.666 90.00 91.57 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 0.037707 0.000000 0.001034 0.00000 SCALE2 0.000000 0.038311 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012557 0.00000 MASTER 243 0 6 0 0 0 0 6 0 0 0 18 END