HEADER STRUCTURAL PROTEIN 28-NOV-00 1G9W TITLE STRUCTURAL BASIS OF COLLAGEN STABILIZATION INDUCED BY PROLINE TITLE 2 HYDROXYLATION 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, C; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES KEYWDS COLLAGEN, EXTRACELLULAR MATRIX, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.VITAGLIANO,R.BERISIO,L.MAZZARELLA,A.ZAGARI REVDAT 5 03-APR-24 1G9W 1 REMARK REVDAT 4 07-FEB-24 1G9W 1 REMARK REVDAT 3 24-FEB-09 1G9W 1 VERSN REVDAT 2 01-APR-03 1G9W 1 JRNL REVDAT 1 18-APR-01 1G9W 0 JRNL AUTH L.VITAGLIANO,R.BERISIO,L.MAZZARELLA,A.ZAGARI JRNL TITL STRUCTURAL BASES OF COLLAGEN STABILIZATION INDUCED BY JRNL TITL 2 PROLINE HYDROXYLATION. JRNL REF BIOPOLYMERS V. 58 459 2001 JRNL REFN ISSN 0006-3525 JRNL PMID 11241217 JRNL DOI 10.1002/1097-0282(20010415)58:5<459::AID-BIP1021>3.0.CO;2-V REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.BERISIO,L.VITAGLIANO,G.SORRENTINO,L.CAROTENUTO,C.PICCOLO, REMARK 1 AUTH 2 L.MAZZARELLA,A.ZAGARI REMARK 1 TITL EFFECTS OF MICROGRAVITY ON THE CRYSTAL QUALITY OF A REMARK 1 TITL 2 COLLAGEN-LIKE POLYPEPTIDE REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 56 55 2000 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444999014158 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.Z.KRAMER,L.VITAGLIANO,J.BELLA,R.BERISIO,L.MAZZARELLA, REMARK 1 AUTH 2 B.BRODSKY,A.ZAGARI,H.M.BERMAN REMARK 1 TITL X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE REMARK 1 TITL 2 PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY) REMARK 1 REF J.MOL.BIOL. V. 280 623 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1998.1881 REMARK 2 REMARK 2 RESOLUTION. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.0 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) : 0.147 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 20.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 320 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)) : 0.146 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 20 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 309 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 126 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 162.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 147 REMARK 3 NUMBER OF RESTRAINTS : 179 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 ANGLE DISTANCES (A) : 0.026 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 DUE TO THE QUASI-INFINITE NATURE OF THE TRIPLE HELIX, DURING REMARK 3 REFINEMENT COVALENT BONDS ARE NECESSARY TO JOIN THE MOLECULE WITH REMARK 3 ITS SYMMETRY MATES BOTH ABOVE IT AND BELOW IT ALONG THE HELICAL REMARK 3 AXIS AND TIGHT REFINEMENT CONSTRAINTS WERE MAINTAINED. REMARK 3 REMARK 3 THE UNIT CELL AXES WERE CHOSEN TO COINCIDE WITH A REMARK 3 PREVIOUS STRUCTURE DETERMINATION (OKUYAMA 1981) OF THIS REMARK 3 PEPTIDE. REMARK 4 REMARK 4 1G9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-00. REMARK 100 THE DEPOSITION ID IS D_1000012415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-98 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.004 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3448 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.04200 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) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 66.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.09300 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB1A3J.ENT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, ACETIC ACID, DIALYSIS, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 13.44350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 10.14400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.17000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 10.14400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.44350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 13.17000 REMARK 290 SMTRY3 4 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 21 RESIDUE ASYMMETRIC UNIT CORRESPONDS TO ONE REMARK 300 TRIPLE-HELICAL REPEAT AND IS SMALLER THAN THE ENTIRE 90 REMARK 300 RESIDUE PEPTIDE. REMARK 300 THE RESULT IS A POLYMER-LIKE STRUCTURE WITH REMARK 300 NO DEFINED ENDS. REMARK 300 REMARK 300 THE POLYMER STRUCTURE IS FORMED BY CONTINUATION OF THE REMARK 300 CHAINS USING THE SYMMETRY-RELATED MOLECULES ALONG THE REMARK 300 HELICAL AXIS. THE TVECT RECORD BELOW PRESENTS THE REMARK 300 TRANSLATION THAT WILL GENERATE THE POLYMER. NOTE: REMARK 300 THEREFORE, CLOSE CONTACTS BETWEEN SYMMETRY-RELATED REMARK 300 MOLECULES ARE INTENTIONAL AND NECESSARY. INTERCHAIN REMARK 300 HYDROGEN BONDING AT THE END OF CHAINS ALSO UTILIZES REMARK 300 SYMMETRY-RELATED MOLECULES. REMARK 300 REMARK 300 THE ENTIRE 30 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 CHAIN A: TRANSLATE RESIDUES 1 - 9 BY (0 0 1), (0 0 2), AND REMARK 300 (0 0 3) AND RESIDUES 7 - 9 BY (0 0 4). REMARK 300 CHAIN B: TRANSLATE RESIDUES 31 - 36 BY (0 0 1), (0 0 2), REMARK 300 AND (0 0 3). REMARK 300 CHAIN C: TRANSLATE RESIDUES 61 - 66 BY (0 0 1), (0 0 2), REMARK 300 AND (0 0 3) AND RESIDUES 64 - 66 BY (004). REMARK 300 THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 90 RESIDUES, REMARK 300 30 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 1540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 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 400 REMARK 400 COMPOUND REMARK 400 HYDROGEN BONDS BETWEEN PEPTIDE CHAINS FOLLOW THE RICH AND REMARK 400 CRICK MODEL II FOR COLLAGEN. 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 N PRO A 1 C GLY B 36 1556 1.30 REMARK 500 N PRO B 31 C GLY C 66 1556 1.34 REMARK 500 C GLY A 9 N PRO C 61 1554 1.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A3J RELATED DB: PDB REMARK 900 RELATED ID: 1A3I RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 FOR EACH CHAIN, RESIDUE NUMBERING CORRESPONDS TO THE ENTIRE REMARK 999 MOLECULE RATHER THAN THE SHORTER ASYMMETRIC UNIT. DBREF 1G9W A 1 9 PDB 1G9W 1G9W 1 9 DBREF 1G9W B 31 36 PDB 1G9W 1G9W 31 36 DBREF 1G9W C 61 66 PDB 1G9W 1G9W 61 66 SEQRES 1 A 9 PRO PRO GLY PRO PRO GLY PRO PRO GLY SEQRES 1 B 6 PRO PRO GLY PRO PRO GLY SEQRES 1 C 6 PRO PRO GLY PRO PRO GLY FORMUL 4 HOH *36(H2 O) CRYST1 26.887 26.340 20.288 90.00 90.00 90.00 P 21 21 21 8 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 0.037193 0.000000 0.000000 0.00000 SCALE2 0.000000 0.037965 0.000000 0.00000 SCALE3 0.000000 0.000000 0.049290 0.00000