HEADER EXTRACELLULAR MATRIX 22-JAN-98 1A3J TITLE X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE TITLE 2 PEPTIDE WITH THE REPEATING SEQUENCE (PRO-PRO-GLY) 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 MOL_ID: 2 KEYWDS COLLAGEN, EXTRACELLULAR MATRIX EXPDTA X-RAY DIFFRACTION AUTHOR R.Z.KRAMER,L.VITAGLIANO,J.BELLA,R.BERISIO,L.MAZZARELLA, AUTHOR 2 B.BRODSKY,A.ZAGARI,H.M.BERMAN REVDAT 3 24-FEB-09 1A3J 1 VERSN REVDAT 2 23-JUN-99 1A3J 1 JRNL REVDAT 1 06-MAY-98 1A3J 0 JRNL AUTH R.Z.KRAMER,L.VITAGLIANO,J.BELLA,R.BERISIO, JRNL AUTH 2 L.MAZZARELLA,B.BRODSKY,A.ZAGARI,H.M.BERMAN JRNL TITL X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A JRNL TITL 2 COLLAGEN-LIKE PEPTIDE WITH THE REPEATING SEQUENCE JRNL TITL 3 (PRO-PRO-GLY). JRNL REF J.MOL.BIOL. V. 280 623 1998 JRNL REFN ISSN 0022-2836 JRNL PMID 9677293 JRNL DOI 10.1006/JMBI.1998.1881 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 1736 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL 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 : 40 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.80 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 1.99 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DUE TO THE QUASI-INFINITE NATURE OF REMARK 3 THE TRIPLE HELIX, DURING REFINEMENT COVALENT BONDS ARE REMARK 3 NECESSARY TO JOIN THE MOLECULE WITH ITS SYMMETRY MATES BOTH REMARK 3 ABOVE IT AND BELOW IT ALONG THE HELICAL AXIS AND TIGHT REMARK 3 REFINEMENT CONSTRAINTS WERE MAINTAINED. THE UNIT CELL AXES REMARK 3 WERE CHOSEN TO COINCIDE WITH A PREVIOUS STRUCTURE REMARK 3 DETERMINATION (OKUYAMA 1981) OF THIS PEPTIDE. REMARK 4 REMARK 4 1A3J COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-94 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : A1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : PRINCETON 2K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL (SCALEPACK) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1836 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.04900 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) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEPTIDE WAS CRYSTALIZED FROM 7.5 REMARK 280 MG/ML PEPTIDE (DISSOLVED IN 5% V/V AQUEOUS ACETIC ACID) AND REMARK 280 0.05 M SODIUM ACETATE. 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 13.50500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 10.21000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 10.21000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.50500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 13.21000 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: REMARK 300 THE 21 RESIDUE ASYMMETRIC UNIT CORRESPONDS TO ONE REMARK 300 TRIPLE-HELICAL REPEAT AND IS SMALLER THAN THE ENTIRE 90 REMARK 300 RESIDUE PEPTIDE DUE TO TRANSLATIONAL DISORDER ALONG THE REMARK 300 HELICAL AXIS. 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: PENTADECAMERIC 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 20.42000 REMARK 350 BIOMT1 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 40.84000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 61.26000 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 81.68000 REMARK 400 REMARK 400 COMPOUND REMARK 400 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 C GLY A 9 N PRO C 61 1554 1.33 REMARK 500 REMARK 500 REMARK: NULL 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 B 243 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH C 242 DISTANCE = 5.80 ANGSTROMS REMARK 999 REMARK 999 SEQUENCE REMARK 999 REMARK 999 FOR EACH CHAIN, RESIDUE NUMBERING CORRESPONDS TO THE ENTIRE REMARK 999 MOLECULE RATHER THAN THE SHORTER ASYMMETRIC UNIT. DBREF 1A3J A 1 9 PDB 1A3J 1A3J 1 9 DBREF 1A3J B 31 36 PDB 1A3J 1A3J 31 36 DBREF 1A3J C 61 66 PDB 1A3J 1A3J 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 *40(H2 O) LINK N PRO C 61 C GLY A 9 1555 1556 1.33 LINK N PRO A 1 C GLY B 36 1555 1556 1.32 LINK N PRO B 31 C GLY C 66 1555 1556 1.34 CRYST1 27.010 26.420 20.420 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 0.037023 0.000000 0.000000 0.00000 SCALE2 0.000000 0.037850 0.000000 0.00000 SCALE3 0.000000 0.000000 0.048972 0.00000 TVECT 1 0.00000 0.00000 20.42000