PDB Short entry for 2LLP HEADER STRUCTURAL PROTEIN, CONTRACTILE PROTEIN 15-NOV-11 2LLP TITLE SOLUTION STRUCTURE OF A THP TYPE 1 ALPHA 1 COLLAGEN FRAGMENT (772-786) COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN ALPHA-1(I) CHAIN; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 949-965; COMPND 5 SYNONYM: ALPHA-1 TYPE I COLLAGEN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 OTHER_DETAILS: SYNTHESIS FROM FMOC SOLID-PHASE CHEMISTRY KEYWDS TRIPLE HELICAL PEPTIDE, STRUCTURAL PROTEIN, CONTRACTILE PROTEIN EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR I.BERTINI,M.FRAGAI,C.LUCHINAT,M.MELIKIAN,M.TOCCAFONDI,J.L.LAUER, AUTHOR 2 G.B.FIELDS REVDAT 1 30-MAY-12 2LLP 0 JRNL AUTH I.BERTINI,M.FRAGAI,C.LUCHINAT,M.MELIKIAN,M.TOCCAFONDI, JRNL AUTH 2 J.L.LAUER,G.B.FIELDS JRNL TITL STRUCTURAL BASIS FOR MATRIX METALLOPROTEINASE 1-CATALYZED JRNL TITL 2 COLLAGENOLYSIS. JRNL REF J.AM.CHEM.SOC. V. 134 2100 2012 JRNL REFN ISSN 0002-7863 JRNL PMID 22239621 JRNL DOI 10.1021/JA208338J REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.0, AMBER 8.0 REMARK 3 AUTHORS : GUNTERT P. (CYANA), CASE, DARDEN, CHEATHAM III, REMARK 3 SIMMERLING, WANG, DUKE, LUO, AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANNEALING AND STRUCTURE CALCULATION REMARK 3 FROM CONSTRAINTS, MINIMISATION BY USING AMBER FORCE FIELD AND REMARK 3 KEEPING THE CONSTRAINTS REMARK 4 REMARK 4 2LLP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-12. REMARK 100 THE RCSB ID CODE IS RCSB102535. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.4-0.8 MM [U-98% 13C; U-98% REMARK 210 15N] THP TYPE I COLLAGEN, 150 MM REMARK 210 SODIUM CHLORIDE, 10 MM CALCIUM REMARK 210 CHLORIDE, 0.1 MM ZINC CHLORIDE, REMARK 210 20 MM [U-2H] TRIS BUFFER, 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 2D 1H- REMARK 210 15N HSQC; 3D HNCA; 3D CBCA(CO)NH; REMARK 210 3D HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.0 REMARK 210 METHOD USED : SIMULATED ANNEALING, MINIMISATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 900 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-30 REMARK 465 RES C SSSEQI REMARK 465 PRO A 11 REMARK 465 PRO A 12 REMARK 465 PRO B 11 REMARK 465 GLY B 28 REMARK 465 PRO C 27 REMARK 465 GLY C 28 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 1 PRO B 12 CA - N - CD ANGL. DEV. = -8.5 DEGREES REMARK 500 3 PRO B 12 CA - N - CD ANGL. DEV. = -9.0 DEGREES REMARK 500 3 ARG B 21 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG B 21 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 5 PRO B 12 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 5 ARG B 21 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 PRO B 12 CA - N - CD ANGL. DEV. = -8.9 DEGREES REMARK 500 8 PRO B 12 CA - N - CD ANGL. DEV. = -8.6 DEGREES REMARK 500 8 ARG B 21 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 9 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 PRO B 12 CA - N - CD ANGL. DEV. = -8.8 DEGREES REMARK 500 10 PRO B 12 CA - N - CD ANGL. DEV. = -8.6 DEGREES REMARK 500 11 PRO B 12 CA - N - CD ANGL. DEV. = -8.8 DEGREES REMARK 500 13 ARG A 21 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 13 PRO B 12 CA - N - CD ANGL. DEV. = -8.5 DEGREES REMARK 500 15 PRO B 12 CA - N - CD ANGL. DEV. = -8.6 DEGREES REMARK 500 15 ARG B 21 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG B 21 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 16 ARG B 21 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 18 PRO B 12 CA - N - CD ANGL. DEV. = -8.8 DEGREES REMARK 500 20 PRO B 12 CA - N - CD ANGL. DEV. = -8.6 DEGREES REMARK 500 21 PRO B 12 CA - N - CD ANGL. DEV. = -9.0 DEGREES REMARK 500 23 PRO B 12 CA - N - CD ANGL. DEV. = -8.6 DEGREES REMARK 500 23 ARG C 21 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 24 PRO B 12 CA - N - CD ANGL. DEV. = -9.4 DEGREES REMARK 500 25 PRO B 12 CA - N - CD ANGL. DEV. = -8.6 DEGREES REMARK 500 26 PRO B 12 CA - N - CD ANGL. DEV. = -8.8 DEGREES REMARK 500 27 PRO B 12 CA - N - CD ANGL. DEV. = -8.6 DEGREES REMARK 500 28 PRO B 12 CA - N - CD ANGL. DEV. = -8.6 DEGREES REMARK 500 29 PRO B 12 CA - N - CD ANGL. DEV. = -8.7 DEGREES REMARK 500 30 ARG A 21 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 30 PRO B 12 CA - N - CD ANGL. DEV. = -9.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 1 PRO A 27 -166.04 -78.19 REMARK 500 1 PRO C 12 -130.07 -73.18 REMARK 500 1 GLN C 15 137.44 166.83 REMARK 500 2 GLN A 15 -166.96 -76.32 REMARK 500 2 PRO A 27 -138.11 -83.17 REMARK 500 2 PRO C 12 -138.87 -71.78 REMARK 500 2 GLN C 15 141.12 171.61 REMARK 500 3 VAL A 24 158.83 -48.44 REMARK 500 3 PRO A 27 -158.26 -79.74 REMARK 500 3 PRO C 12 -132.24 -71.37 REMARK 500 3 GLN C 15 138.35 175.26 REMARK 500 4 GLN A 15 -152.16 -94.95 REMARK 500 4 PRO A 27 -158.22 -75.98 REMARK 500 4 PRO C 12 -131.27 -67.56 REMARK 500 4 PRO C 14 -110.00 -78.45 REMARK 500 5 GLN A 15 -177.60 -56.51 REMARK 500 5 VAL A 24 157.96 -46.13 REMARK 500 5 PRO A 27 -169.56 -76.42 REMARK 500 5 GLN B 15 152.38 175.55 REMARK 500 5 PRO C 12 177.41 -50.60 REMARK 500 5 GLN C 15 126.21 -39.25 REMARK 500 5 VAL C 24 -169.68 -100.82 REMARK 500 6 GLN A 15 -179.14 -63.72 REMARK 500 6 VAL A 24 157.22 -47.97 REMARK 500 6 PRO C 12 -169.49 -54.04 REMARK 500 7 GLN A 15 -137.18 -78.90 REMARK 500 7 ALA A 18 46.69 -70.65 REMARK 500 7 PRO A 27 -158.04 -80.24 REMARK 500 7 PRO B 14 -175.01 -68.62 REMARK 500 7 PRO C 12 -163.78 -68.73 REMARK 500 7 GLN C 15 -124.12 67.80 REMARK 500 7 VAL C 24 -169.32 -75.90 REMARK 500 8 PRO A 27 -158.71 -81.90 REMARK 500 8 PRO B 14 -134.99 -77.83 REMARK 500 8 PRO C 12 -137.78 -72.28 REMARK 500 8 GLN C 15 151.52 71.89 REMARK 500 9 PRO A 14 -170.03 -69.16 REMARK 500 9 PRO A 27 -155.60 -79.21 REMARK 500 9 PRO C 12 -174.40 -56.18 REMARK 500 10 GLN A 15 163.73 -46.07 REMARK 500 10 PRO B 14 -123.39 -74.38 REMARK 500 10 PRO C 12 -179.35 -49.58 REMARK 500 10 GLN C 15 147.32 74.70 REMARK 500 11 PRO A 14 -168.65 -71.82 REMARK 500 11 PRO A 27 -165.03 -77.74 REMARK 500 11 GLN B 15 160.58 177.93 REMARK 500 11 PRO C 12 -179.40 -55.94 REMARK 500 11 GLN C 15 120.34 -32.22 REMARK 500 12 GLN A 15 -155.44 -82.58 REMARK 500 12 GLN B 15 143.61 -38.91 REMARK 500 REMARK 500 THIS ENTRY HAS 122 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 27 GLY A 28 2 142.84 REMARK 500 PRO B 12 GLY B 13 3 125.56 REMARK 500 GLY B 13 PRO B 14 3 148.71 REMARK 500 PRO A 27 GLY A 28 4 142.76 REMARK 500 PRO B 12 GLY B 13 5 123.93 REMARK 500 PRO B 12 GLY B 13 6 130.02 REMARK 500 PRO B 12 GLY B 13 8 125.51 REMARK 500 PRO B 12 GLY B 13 9 128.00 REMARK 500 PRO B 12 GLY B 13 10 125.54 REMARK 500 LEU B 26 PRO B 27 10 148.59 REMARK 500 PRO B 12 GLY B 13 11 126.41 REMARK 500 PRO A 27 GLY A 28 13 142.24 REMARK 500 PRO B 12 GLY B 13 13 126.22 REMARK 500 PRO B 12 GLY B 13 14 144.05 REMARK 500 GLY A 19 GLN A 20 15 145.37 REMARK 500 PRO A 27 GLY A 28 15 148.64 REMARK 500 PRO B 12 GLY B 13 15 128.25 REMARK 500 PRO A 27 GLY A 28 16 148.89 REMARK 500 LEU A 26 PRO A 27 17 136.79 REMARK 500 GLY B 25 LEU B 26 17 -148.86 REMARK 500 GLY A 19 GLN A 20 18 141.35 REMARK 500 PRO B 12 GLY B 13 18 143.23 REMARK 500 LEU B 26 PRO B 27 18 146.95 REMARK 500 PRO C 14 GLN C 15 19 -148.04 REMARK 500 PRO B 12 GLY B 13 20 124.76 REMARK 500 PRO C 14 GLN C 15 20 148.11 REMARK 500 PRO B 12 GLY B 13 21 138.98 REMARK 500 GLY A 19 GLN A 20 22 127.77 REMARK 500 LEU A 26 PRO A 27 22 148.03 REMARK 500 PRO A 27 GLY A 28 24 143.67 REMARK 500 PRO B 12 GLY B 13 24 127.56 REMARK 500 PRO B 12 GLY B 13 26 149.72 REMARK 500 PRO B 12 GLY B 13 28 127.47 REMARK 500 GLY C 25 LEU C 26 28 146.12 REMARK 500 PRO B 12 GLY B 13 29 123.92 REMARK 500 GLN B 15 GLY B 16 29 149.41 REMARK 500 PRO A 27 GLY A 28 30 141.90 REMARK 500 PRO B 12 GLY B 13 30 128.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 4 ARG A 21 0.16 SIDE CHAIN REMARK 500 12 ARG B 21 0.08 SIDE CHAIN REMARK 500 14 ARG C 21 0.10 SIDE CHAIN REMARK 500 17 ARG A 21 0.08 SIDE CHAIN REMARK 500 19 ARG C 21 0.08 SIDE CHAIN REMARK 500 28 ARG C 21 0.08 SIDE CHAIN REMARK 500 29 ARG B 21 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18083 RELATED DB: BMRB DBREF 2LLP A 12 28 UNP P02452 CO1A1_HUMAN 949 965 DBREF 2LLP B 12 28 UNP P02452 CO1A1_HUMAN 949 965 DBREF 2LLP C 12 28 UNP P02452 CO1A1_HUMAN 949 965 SEQADV 2LLP PRO A 11 UNP P02452 EXPRESSION TAG SEQADV 2LLP PRO B 11 UNP P02452 EXPRESSION TAG SEQADV 2LLP PRO C 11 UNP P02452 EXPRESSION TAG SEQRES 1 A 18 PRO PRO GLY PRO GLN GLY ILE ALA GLY GLN ARG GLY VAL SEQRES 2 A 18 VAL GLY LEU PRO GLY SEQRES 1 B 18 PRO PRO GLY PRO GLN GLY ILE ALA GLY GLN ARG GLY VAL SEQRES 2 B 18 VAL GLY LEU PRO GLY SEQRES 1 C 18 PRO PRO GLY PRO GLN GLY ILE ALA GLY GLN ARG GLY VAL SEQRES 2 C 18 VAL GLY LEU PRO GLY CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000