10 20 30 40 50 60 70 80 2CUO - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL PROTEIN 27-MAY-05 2CUO
TITLE COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9
COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN MODEL PEPTIDE (PRO-PRO-GLY)9; 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: COLLAGEN MODEL PEPTIDE WAS CHEMICALLY SOURCE 4 SYSTHESIZED
KEYWDS COLLAGEN MODEL PEPTIDE, TRIPLE-HELIX, PUCKERING, STRUCTURAL KEYWDS 2 PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR C.HONGO,K.NOGUCHI,K.OKUYAMA,Y.TANAKA,N.NISHINO
REVDAT 3 24-FEB-09 2CUO 1 VERSN REVDAT 2 24-JAN-06 2CUO 1 JRNL REVDAT 1 14-JUN-05 2CUO 0
JRNL AUTH C.HONGO,K.NOGUCHI,K.OKUYAMA,Y.TANAKA,N.NISHINO JRNL TITL REPETITIVE INTERACTIONS OBSERVED IN THE CRYSTAL JRNL TITL 2 STRUCTURE OF A COLLAGEN-MODEL PEPTIDE, JRNL TITL 3 [(PRO-PRO-GLY)9]3 JRNL REF J.BIOCHEM.(TOKYO) V. 138 135 2005 JRNL REFN ISSN 0021-924X JRNL PMID 16091587 JRNL DOI 10.1093/JB/MVI108
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.33 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) : 1.33 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 CROSS-VALIDATION METHOD : NULL 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) : 0.184 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.182 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1185 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 24205 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.172 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.170 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 890 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 18016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 958 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 332 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1290.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 918.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 9953 REMARK 3 NUMBER OF RESTRAINTS : 12321 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 ANGLE DISTANCES (A) : 0.023 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.056 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.042 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.008 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.003 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.045 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.034 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOTROPIC REFINEMENT REDUCED FREE R
REMARK 4 REMARK 4 2CUO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUN-05. REMARK 100 THE RCSB ID CODE IS RCSB024639.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-01 REMARK 200 TEMPERATURE (KELVIN) : 100.0 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 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24336 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.330 REMARK 200 RESOLUTION RANGE LOW (A) : 25.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.33 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.26900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 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: PDB ENTRY 1ITT REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400, 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 13.28150 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, 3 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: 4420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4250 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: 4380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -72.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, 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 GLY A 127 REMARK 465 GLY B 227 REMARK 465 GLY D 427 REMARK 465 GLY E 527
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 E2132 DISTANCE = 5.67 ANGSTROMS REMARK 525 HOH E2178 DISTANCE = 5.14 ANGSTROMS
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ITT RELATED DB: PDB REMARK 900 AVERAGE CRYSTAL STRUCTURE OF (PRO-PRO-GLY)9
DBREF 2CUO A 101 127 PDB 2CUO 2CUO 101 127 DBREF 2CUO B 201 227 PDB 2CUO 2CUO 201 227 DBREF 2CUO C 301 327 PDB 2CUO 2CUO 301 327 DBREF 2CUO D 401 427 PDB 2CUO 2CUO 401 427 DBREF 2CUO E 501 527 PDB 2CUO 2CUO 501 527 DBREF 2CUO F 601 627 PDB 2CUO 2CUO 601 627
SEQRES 1 A 27 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO SEQRES 2 A 27 PRO 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 PRO 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 PRO 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 PRO 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 PRO 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 PRO SEQRES 2 F 27 PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 F 27 GLY
FORMUL 7 HOH *332(H2 O)
CRYST1 25.946 26.563 80.140 90.00 90.00 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 0.038542 0.000000 0.000000 0.00000
SCALE2 0.000000 0.037646 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012478 0.00000