HEADER EXTRACELLULAR MATRIX 22-JAN-98 1A3I TITLE X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE PEPTIDE WITH TITLE 2 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,B.BRODSKY, AUTHOR 2 A.ZAGARI,H.M.BERMAN REVDAT 6 23-OCT-24 1A3I 1 REMARK REVDAT 5 03-APR-24 1A3I 1 REMARK LINK REVDAT 4 18-APR-18 1A3I 1 REMARK REVDAT 3 24-FEB-09 1A3I 1 VERSN REVDAT 2 23-JUN-99 1A3I 1 JRNL REVDAT 1 06-MAY-98 1A3I 0 JRNL AUTH R.Z.KRAMER,L.VITAGLIANO,J.BELLA,R.BERISIO,L.MAZZARELLA, JRNL AUTH 2 B.BRODSKY,A.ZAGARI,H.M.BERMAN JRNL TITL X-RAY CRYSTALLOGRAPHIC DETERMINATION OF A COLLAGEN-LIKE JRNL TITL 2 PEPTIDE WITH THE REPEATING SEQUENCE (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 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.1000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 76.7 REMARK 3 NUMBER OF REFLECTIONS : 861 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) : 0.181 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 : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 69 REMARK 3 BIN R VALUE (WORKING SET) : 0.2200 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 : 8 REMARK 3 SOLVENT ATOMS : 37 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.90 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) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 2.070 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 2.110 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : GROUP 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 DUE TO THE QUASI-INFINITE, AVERAGED NATURE OF THE TRIPLE HELIX, REMARK 3 DURING REFINEMENT COVALENT BONDS ARE NECESSARY TO JOIN THE REMARK 3 MOLECULE WITH ITS SYMMETRY MATES BOTH ABOVE IT AND BELOW IT ALONG REMARK 3 THE HELICAL 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 1A3I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170346. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : OCT-91 REMARK 200 TEMPERATURE (KELVIN) : 259.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS FAST REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOLEN REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 1136 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: IDEALIZED SEVEN-FOLD TRIPLE-HELIX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEPTIDE WAS CRYSTALLIZED FROM 4.0 REMARK 280 MG/ML PEPTIDE IN 10% ACETIC ACID, 0.1% SODIUM AZIDE, AND 3.0% REMARK 280 PEG400. 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 13.41000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 10.09000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.14500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 10.09000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.41000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 13.14500 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 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 20.18000 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 40.36000 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 60.54000 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 80.72000 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: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 PRO A 2 171.52 -56.35 REMARK 500 PRO A 5 164.30 -47.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY C 402 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 1A3I A 1 9 PDB 1A3I 1A3I 1 9 DBREF 1A3I B 31 36 PDB 1A3I 1A3I 31 36 DBREF 1A3I C 61 66 PDB 1A3I 1A3I 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 HET ACY A 401 4 HET ACY C 402 4 HETNAM ACY ACETIC ACID FORMUL 4 ACY 2(C2 H4 O2) FORMUL 6 HOH *37(H2 O) LINK N PRO A 1 C GLY B 36 1555 1556 1.34 LINK C GLY A 9 N PRO C 61 1556 1555 1.31 LINK N PRO B 31 C GLY C 66 1555 1556 1.33 SITE 1 AC1 7 PRO A 5 PRO A 8 HOH A 103 HOH A 218 SITE 2 AC1 7 PRO C 64 HOH C 122 ACY C 402 SITE 1 AC2 5 ACY A 401 PRO B 34 HOH B 247 HOH C 122 SITE 2 AC2 5 HOH C 202 CRYST1 26.820 26.290 20.180 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 0.037286 0.000000 0.000000 0.00000 SCALE2 0.000000 0.038037 0.000000 0.00000 SCALE3 0.000000 0.000000 0.049554 0.00000