HEADER PROTEIN BINDING 05-DEC-18 6Q43 TITLE ATOMIC RESOLUTION CRYSTAL STRUCTURE OF AN ABA COLLAGEN HETEROTRIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEADING CHAIN OF THE ABA COLLAGEN HETEROTRIMER; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MIDDLE CHAIN OF THE ABA COLLAGEN HETEROTRIMER; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: TRAILING CHAIN OF THE ABA COLLAGEN HETEROTRIMER; COMPND 11 CHAIN: C; COMPND 12 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 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS COLLAGEN 1, HETEROTRIMER, DISCOIDIN DOMAIN RECEPTOR, VON WILLEBRAND KEYWDS 2 FACTOR, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.A.JALAN,J.D.HARTGERINK,P.BREAR,B.LEITINGER,R.W.FARNDALE REVDAT 2 24-JAN-24 6Q43 1 REMARK REVDAT 1 18-DEC-19 6Q43 0 JRNL AUTH A.A.JALAN,J.D.HARTGERINK,P.BREAR,B.LEITINGER,R.W.FARNDALE JRNL TITL ATOMIC RESOLUTION CRYSTAL STRUCTURE OF AN AAB COLLAGEN JRNL TITL 2 HETEROTRIMER JRNL REF NAT.CHEM.BIOL. 2019 JRNL REFN ESSN 1552-4469 JRNL DOI 10.1038/S41589-019-0435-Y REMARK 2 REMARK 2 RESOLUTION. 1.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 33742 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.177 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1733 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 64.5100 - 2.6600 0.99 2813 159 0.1449 0.1691 REMARK 3 2 2.6600 - 2.1100 0.99 2765 168 0.1338 0.1713 REMARK 3 3 2.1100 - 1.8400 0.99 2745 132 0.1161 0.1536 REMARK 3 4 1.8400 - 1.6700 0.98 2701 150 0.1279 0.1680 REMARK 3 5 1.6700 - 1.5500 0.98 2683 142 0.1295 0.1714 REMARK 3 6 1.5500 - 1.4600 0.97 2655 147 0.1389 0.1609 REMARK 3 7 1.4600 - 1.3900 0.96 2666 143 0.1359 0.1729 REMARK 3 8 1.3900 - 1.3300 0.96 2623 131 0.1590 0.1947 REMARK 3 9 1.3300 - 1.2800 0.96 2638 140 0.1770 0.2059 REMARK 3 10 1.2800 - 1.2300 0.95 2638 113 0.2077 0.2427 REMARK 3 11 1.2300 - 1.1900 0.95 2565 145 0.2175 0.2807 REMARK 3 12 1.1900 - 1.1600 0.93 2517 163 0.2434 0.2780 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.104 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.423 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.49 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 973 REMARK 3 ANGLE : 1.182 1329 REMARK 3 CHIRALITY : 0.070 101 REMARK 3 PLANARITY : 0.006 206 REMARK 3 DIHEDRAL : 11.973 418 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6Q43 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200013264. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 20161205 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32, CCP4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33812 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 64.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 1.50300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.7.17, CCP4 REMARK 200 STARTING MODEL: 1V7H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG 3350, 0.2M SODIUM NITRATE, PH REMARK 280 8.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 13.32600 REMARK 290 SMTRY3 2 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 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: 9320 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 154 O HOH C 260 2.06 REMARK 500 O HOH B 116 O HOH B 154 2.16 REMARK 500 O HOH C 253 O HOH C 259 2.16 REMARK 500 O HOH A 233 O HOH A 259 2.19 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 A 279 DISTANCE = 6.60 ANGSTROMS REMARK 525 HOH B 180 DISTANCE = 6.15 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6Q3P RELATED DB: PDB REMARK 900 6Q3P IS AN AAB HETEROTRIMER I.E. THE CHAIN ARRANGEMENT WITHIN THE REMARK 900 TRIPLE HELIX IS DIFFERENT REMARK 900 RELATED ID: 6Q41 RELATED DB: PDB REMARK 900 6Q41 IS AN ABA HETEROTRIMER I.E. THE CHAIN ARRANGEMENT WITHIN THE REMARK 900 TRIPLE HELIX IS DIFFERENT DBREF 6Q43 A 1 46 PDB 6Q43 6Q43 1 46 DBREF 6Q43 B 0 46 PDB 6Q43 6Q43 0 46 DBREF 6Q43 C 0 45 PDB 6Q43 6Q43 0 45 SEQRES 1 A 46 GLY PRO PRO GLY PRO LYS GLY PRO LYS GLY ASP PRO GLY SEQRES 2 A 46 ASP PRO GLY PRO PRO GLY ALA ARG GLY GLN ALA GLY VAL SEQRES 3 A 46 NLE GLY PHE HYP GLY PRO PRO GLY PRO LYS GLY PRO LYS SEQRES 4 A 46 GLY ASP PRO GLY ASP PRO GLY SEQRES 1 B 47 ACE GLY PRO PRO GLY PRO PRO GLY ASP LYS GLY ASP LYS SEQRES 2 B 47 GLY PRO PRO GLY PRO PRO GLY ALA ARG GLY GLU HYP GLY SEQRES 3 B 47 ASN ILE GLY PHE HYP GLY PRO PRO GLY PRO PRO GLY ASP SEQRES 4 B 47 LYS GLY ASP LYS GLY PRO PRO GLY SEQRES 1 C 46 ACE GLY PRO PRO GLY PRO LYS GLY PRO LYS GLY ASP PRO SEQRES 2 C 46 GLY ASP PRO GLY PRO PRO GLY ALA ARG GLY GLN ALA GLY SEQRES 3 C 46 VAL NLE GLY PHE HYP GLY PRO PRO GLY PRO LYS GLY PRO SEQRES 4 C 46 LYS GLY ASP PRO GLY ASP PRO HET NLE A 27 18 HET HYP A 30 15 HET ACE B 0 6 HET HYP B 24 15 HET HYP B 30 15 HET ACE C 0 6 HET NLE C 27 18 HET HYP C 30 15 HET GOL A 101 14 HET GOL C 101 14 HETNAM NLE NORLEUCINE HETNAM HYP 4-HYDROXYPROLINE HETNAM ACE ACETYL GROUP HETNAM GOL GLYCEROL HETSYN HYP HYDROXYPROLINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 NLE 2(C6 H13 N O2) FORMUL 1 HYP 4(C5 H9 N O3) FORMUL 2 ACE 2(C2 H4 O) FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 HOH *235(H2 O) LINK C VAL A 26 N NLE A 27 1555 1555 1.33 LINK C NLE A 27 N GLY A 28 1555 1555 1.33 LINK C PHE A 29 N HYP A 30 1555 1555 1.33 LINK C HYP A 30 N GLY A 31 1555 1555 1.33 LINK C ACE B 0 N GLY B 1 1555 1555 1.33 LINK C GLU B 23 N HYP B 24 1555 1555 1.33 LINK C HYP B 24 N GLY B 25 1555 1555 1.33 LINK C PHE B 29 N HYP B 30 1555 1555 1.33 LINK C HYP B 30 N GLY B 31 1555 1555 1.33 LINK C ACE C 0 N GLY C 1 1555 1555 1.33 LINK C VAL C 26 N NLE C 27 1555 1555 1.33 LINK C NLE C 27 N GLY C 28 1555 1555 1.32 LINK C PHE C 29 N HYP C 30 1555 1555 1.33 LINK C HYP C 30 N GLY C 31 1555 1555 1.33 SITE 1 AC1 4 HYP A 30 HOH A 218 HOH A 231 HOH A 248 SITE 1 AC2 8 NLE C 27 PHE C 29 LYS C 36 GLY C 37 SITE 2 AC2 8 HOH C 203 HOH C 211 HOH C 245 HOH C 250 CRYST1 29.339 26.652 64.457 90.00 92.24 90.00 P 1 21 1 2 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 0.034084 0.000000 0.001333 0.00000 SCALE2 0.000000 0.037521 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015526 0.00000