HEADER STRUCTURAL PROTEIN 16-OCT-01 1K6F TITLE CRYSTAL STRUCTURE OF THE COLLAGEN TRIPLE HELIX MODEL [(PRO-PRO-GLY) TITLE 2 10]3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN TRIPLE HELIX; 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: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. KEYWDS COLLAGEN STABILITY, PUCKERING, AMINO ACID PREFERENCES, TRIPLE HELIX, KEYWDS 2 STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.BERISIO,L.VITAGLIANO,L.MAZZARELLA,A.ZAGARI REVDAT 6 07-FEB-24 1K6F 1 REMARK REVDAT 5 31-JAN-18 1K6F 1 REMARK REVDAT 4 24-JAN-18 1K6F 1 AUTHOR JRNL REVDAT 3 24-FEB-09 1K6F 1 VERSN REVDAT 2 01-APR-03 1K6F 1 JRNL REVDAT 1 30-JAN-02 1K6F 0 JRNL AUTH R.BERISIO,L.VITAGLIANO,L.MAZZARELLA,A.ZAGARI JRNL TITL CRYSTAL STRUCTURE OF THE COLLAGEN TRIPLE HELIX MODEL JRNL TITL 2 [(PRO-PRO-GLY)(10)](3) JRNL REF PROTEIN SCI. V. 11 262 2002 JRNL REFN ISSN 0961-8368 JRNL PMID 11790836 JRNL DOI 10.1110/PS.32602 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.VITAGLIANO,R.BERISIO,A.MASTRANGELO,L.MAZZARELLA,A.ZAGARI REMARK 1 TITL PREFERRED PROLINE PUCKERING IN CIS AND TRANS PEPTIDE GROUPS: REMARK 1 TITL 2 IMPLICATIONS FOR COLLAGEN STABILITY REMARK 1 REF PROTEIN SCI. V. 10 2627 2001 REMARK 1 REFN ISSN 0961-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH L.VITAGLIANO,R.BERISIO,L.MAZZARELLA,A.ZAGARI REMARK 1 TITL STRUCTURAL BASES OF COLLAGEN STABILIZATION INDUCED BY REMARK 1 TITL 2 PROLINE HYDROXYLATION REMARK 1 REF BIOPOLYMERS V. 58 459 2001 REMARK 1 REFN ISSN 0006-3525 REMARK 1 DOI 10.1002/1097-0282(20010415)58:5<459::AID-BIP1021>3.0.CO;2-V REMARK 1 REFERENCE 3 REMARK 1 AUTH R.BERISIO,L.VITAGLIANO,L.MAZZARELLA,A.ZAGARI REMARK 1 TITL CRYSTAL STRUCTURE OF A COLLAGEN-LIKE POLYPEPTIDE WITH REMARK 1 TITL 2 REPEATING SEQUENCE PRO-HYP-GLY AT 1.4 A RESOLUTION: REMARK 1 TITL 3 IMPLICATIONS FOR COLLAGEN HYDRATION REMARK 1 REF BIOPOLYMERS V. 56 8 2001 REMARK 1 REFN ISSN 0006-3525 REMARK 1 DOI 10.1002/1097-0282(2000)56:1<8::AID-BIP1037>3.0.CO;2-W 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) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL 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) : 0.226 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.185 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1152 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 29431 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)) : 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)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1056 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 349 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.026 REMARK 3 ANGLE DISTANCES (A) : 0.045 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 & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1K6F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-01. REMARK 100 THE DEPOSITION ID IS D_1000014618. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 294; NULL REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ELETTRA; EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : 5.2R; BW7B REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9; 0.87 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; NULL REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23121 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: ARP/WARP REMARK 200 SOFTWARE USED: ARP/WARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HAC/NAAC, PH 5.6, MICRODIALYSIS REMARK 280 CARRIED OUT IN MICROGRAVITY CONDITIONS, TEMPERATURE 21K, REMARK 280 TEMPERATURE 294.0K 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 13.45350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 91.24900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 13.17850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 91.24900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 13.45350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 13.17850 REMARK 290 SMTRY3 4 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: 4790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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: 4790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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: 10610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 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 APPLY THE FOLLOWING TO CHAINS: D, E, F REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 13.45350 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 52.71400 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 91.24900 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 30 REMARK 465 GLY B 30 REMARK 465 GLY C 30 REMARK 465 GLY D 30 REMARK 465 GLY E 30 REMARK 465 GLY F 30 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO F 29 C PRO F 29 O 0.192 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 29 CA - C - O ANGL. DEV. = 18.6 DEGREES REMARK 500 PRO B 29 N - CA - C ANGL. DEV. = 15.7 DEGREES REMARK 500 PRO F 29 N - CA - CB ANGL. DEV. = -7.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 AN APPROPRIATE SEQUENCE DATABASE REMARK 999 REFERENCE WAS NOT AVAILABLE AT REMARK 999 THE TIME OF PROCESSING. DBREF 1K6F A 1 30 PDB 1K6F 1K6F 1 30 DBREF 1K6F B 1 30 PDB 1K6F 1K6F 1 30 DBREF 1K6F C 1 30 PDB 1K6F 1K6F 1 30 DBREF 1K6F D 1 30 PDB 1K6F 1K6F 1 30 DBREF 1K6F E 1 30 PDB 1K6F 1K6F 1 30 DBREF 1K6F F 1 30 PDB 1K6F 1K6F 1 30 SEQRES 1 A 30 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO SEQRES 2 A 30 PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 A 30 GLY PRO PRO GLY SEQRES 1 B 30 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO SEQRES 2 B 30 PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 B 30 GLY PRO PRO GLY SEQRES 1 C 30 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO SEQRES 2 C 30 PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 C 30 GLY PRO PRO GLY SEQRES 1 D 30 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO SEQRES 2 D 30 PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 D 30 GLY PRO PRO GLY SEQRES 1 E 30 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO SEQRES 2 E 30 PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 E 30 GLY PRO PRO GLY SEQRES 1 F 30 PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO SEQRES 2 F 30 PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO GLY PRO PRO SEQRES 3 F 30 GLY PRO PRO GLY FORMUL 7 HOH *349(H2 O) CRYST1 26.907 26.357 182.498 90.00 90.00 90.00 P 21 21 21 24 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 0.037170 0.000000 0.000000 0.00000 SCALE2 0.000000 0.037940 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005480 0.00000