HEADER CELL ADHESION 16-NOV-22 8HHK TITLE CRYSTAL STRUCTURE OF A TRIPLE-HELIX REGION OF HUMAN COLLAGEN TYPE III COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRO-HYP-GLY-PRO-HYP-GLY-PRO-HYP-GLY-PHE-ASP-GLY-ARG-ASN- COMPND 3 GLY-GLU-LYS-GLY; COMPND 4 CHAIN: A, B, C, G, H, I; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS HUMAN COLLAGEN TYPE III, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR Z.C.YAN,D.ZHANG,B.QIN REVDAT 1 18-JAN-23 8HHK 0 JRNL AUTH Z.C.YAN,D.ZHANG,B.QIN JRNL TITL CRYSTAL STRUCTURE OF A TRIPLE-HELIX REGION OF HUMAN COLLAGEN JRNL TITL 2 TYPE III JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.1_3865 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.310 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 3808 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.314 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540 REMARK 3 FREE R VALUE TEST SET COUNT : 173 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 2.5600 - 2.5000 0.96 3635 173 0.2511 0.3138 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.357 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.102 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 5.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.39 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 : 0.010 1005 REMARK 3 ANGLE : 1.487 1364 REMARK 3 CHIRALITY : 0.101 122 REMARK 3 PLANARITY : 0.010 187 REMARK 3 DIHEDRAL : 30.264 359 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 8HHK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1300033630. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-SEP-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3808 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07236 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.06429 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 15.24 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 28.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES SODIUM PH 7.5, 2% V/V REMARK 280 POLYETHYLENE GLYCOL 400 2.0 M AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 3610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 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: 4220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: G, H, I 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. (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 GLU A 19 REMARK 465 THR A 20 REMARK 465 GLY A 21 REMARK 465 PRO A 22 REMARK 465 HYP A 23 REMARK 465 GLY A 24 REMARK 465 PRO A 25 REMARK 465 HYP A 26 REMARK 465 GLY A 27 REMARK 465 PRO A 28 REMARK 465 HYP A 29 REMARK 465 GLY A 30 REMARK 465 GLY B 24 REMARK 465 PRO B 25 REMARK 465 HYP B 26 REMARK 465 GLY B 27 REMARK 465 PRO B 28 REMARK 465 HYP B 29 REMARK 465 GLY B 30 REMARK 465 PRO C 28 REMARK 465 HYP C 29 REMARK 465 GLY C 30 REMARK 465 HYP G 23 REMARK 465 GLY G 24 REMARK 465 PRO G 25 REMARK 465 HYP G 26 REMARK 465 GLY G 27 REMARK 465 PRO G 28 REMARK 465 HYP G 29 REMARK 465 GLY G 30 REMARK 465 GLY H 24 REMARK 465 PRO H 25 REMARK 465 HYP H 26 REMARK 465 GLY H 27 REMARK 465 PRO H 28 REMARK 465 HYP H 29 REMARK 465 GLY H 30 REMARK 465 PRO I 25 REMARK 465 HYP I 26 REMARK 465 GLY I 27 REMARK 465 PRO I 28 REMARK 465 HYP I 29 REMARK 465 GLY I 30 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 211 O HOH G 108 2.17 REMARK 500 ND2 ASN H 14 O HOH H 101 2.17 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 LYS B 17 140.14 -36.73 REMARK 500 THR C 20 130.71 -29.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU C 19 17.70 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HHK A 1 30 PDB 8HHK 8HHK 1 30 DBREF 8HHK B 1 30 PDB 8HHK 8HHK 1 30 DBREF 8HHK C 1 30 PDB 8HHK 8HHK 1 30 DBREF 8HHK G 1 30 PDB 8HHK 8HHK 1 30 DBREF 8HHK H 1 30 PDB 8HHK 8HHK 1 30 DBREF 8HHK I 1 30 PDB 8HHK 8HHK 1 30 SEQRES 1 A 30 PRO HYP GLY PRO HYP GLY PRO HYP GLY PHE ASP GLY ARG SEQRES 2 A 30 ASN GLY GLU LYS GLY GLU THR GLY PRO HYP GLY PRO HYP SEQRES 3 A 30 GLY PRO HYP GLY SEQRES 1 B 30 PRO HYP GLY PRO HYP GLY PRO HYP GLY PHE ASP GLY ARG SEQRES 2 B 30 ASN GLY GLU LYS GLY GLU THR GLY PRO HYP GLY PRO HYP SEQRES 3 B 30 GLY PRO HYP GLY SEQRES 1 C 30 PRO HYP GLY PRO HYP GLY PRO HYP GLY PHE ASP GLY ARG SEQRES 2 C 30 ASN GLY GLU LYS GLY GLU THR GLY PRO HYP GLY PRO HYP SEQRES 3 C 30 GLY PRO HYP GLY SEQRES 1 G 30 PRO HYP GLY PRO HYP GLY PRO HYP GLY PHE ASP GLY ARG SEQRES 2 G 30 ASN GLY GLU LYS GLY GLU THR GLY PRO HYP GLY PRO HYP SEQRES 3 G 30 GLY PRO HYP GLY SEQRES 1 H 30 PRO HYP GLY PRO HYP GLY PRO HYP GLY PHE ASP GLY ARG SEQRES 2 H 30 ASN GLY GLU LYS GLY GLU THR GLY PRO HYP GLY PRO HYP SEQRES 3 H 30 GLY PRO HYP GLY SEQRES 1 I 30 PRO HYP GLY PRO HYP GLY PRO HYP GLY PHE ASP GLY ARG SEQRES 2 I 30 ASN GLY GLU LYS GLY GLU THR GLY PRO HYP GLY PRO HYP SEQRES 3 I 30 GLY PRO HYP GLY HET HYP A 2 8 HET HYP A 5 8 HET HYP A 8 8 HET HYP B 2 8 HET HYP B 5 8 HET HYP B 8 8 HET HYP B 23 8 HET HYP C 2 8 HET HYP C 5 8 HET HYP C 8 8 HET HYP C 23 8 HET HYP C 26 8 HET HYP G 2 8 HET HYP G 5 8 HET HYP G 8 8 HET HYP H 2 8 HET HYP H 5 8 HET HYP H 8 8 HET HYP H 23 8 HET HYP I 2 8 HET HYP I 5 8 HET HYP I 8 8 HET HYP I 23 8 HET SO4 B 101 5 HETNAM HYP 4-HYDROXYPROLINE HETNAM SO4 SULFATE ION HETSYN HYP HYDROXYPROLINE FORMUL 1 HYP 23(C5 H9 N O3) FORMUL 7 SO4 O4 S 2- FORMUL 8 HOH *76(H2 O) LINK C PRO A 1 N HYP A 2 1555 1555 1.33 LINK C HYP A 2 N GLY A 3 1555 1555 1.33 LINK C PRO A 4 N HYP A 5 1555 1555 1.32 LINK C HYP A 5 N GLY A 6 1555 1555 1.32 LINK C PRO A 7 N HYP A 8 1555 1555 1.33 LINK C HYP A 8 N GLY A 9 1555 1555 1.33 LINK C PRO B 1 N HYP B 2 1555 1555 1.33 LINK C HYP B 2 N GLY B 3 1555 1555 1.33 LINK C PRO B 4 N HYP B 5 1555 1555 1.33 LINK C HYP B 5 N GLY B 6 1555 1555 1.33 LINK C PRO B 7 N HYP B 8 1555 1555 1.33 LINK C HYP B 8 N GLY B 9 1555 1555 1.34 LINK C PRO B 22 N HYP B 23 1555 1555 1.33 LINK C PRO C 1 N HYP C 2 1555 1555 1.33 LINK C HYP C 2 N GLY C 3 1555 1555 1.33 LINK C PRO C 4 N HYP C 5 1555 1555 1.32 LINK C HYP C 5 N GLY C 6 1555 1555 1.33 LINK C PRO C 7 N HYP C 8 1555 1555 1.32 LINK C HYP C 8 N GLY C 9 1555 1555 1.33 LINK C PRO C 22 N HYP C 23 1555 1555 1.33 LINK C HYP C 23 N GLY C 24 1555 1555 1.33 LINK C PRO C 25 N HYP C 26 1555 1555 1.33 LINK C HYP C 26 N GLY C 27 1555 1555 1.33 LINK C PRO G 1 N HYP G 2 1555 1555 1.33 LINK C HYP G 2 N GLY G 3 1555 1555 1.33 LINK C PRO G 4 N HYP G 5 1555 1555 1.32 LINK C HYP G 5 N GLY G 6 1555 1555 1.33 LINK C PRO G 7 N HYP G 8 1555 1555 1.33 LINK C HYP G 8 N GLY G 9 1555 1555 1.33 LINK C PRO H 1 N HYP H 2 1555 1555 1.33 LINK C HYP H 2 N GLY H 3 1555 1555 1.33 LINK C PRO H 4 N HYP H 5 1555 1555 1.33 LINK C HYP H 5 N GLY H 6 1555 1555 1.33 LINK C PRO H 7 N HYP H 8 1555 1555 1.33 LINK C HYP H 8 N GLY H 9 1555 1555 1.34 LINK C PRO H 22 N HYP H 23 1555 1555 1.33 LINK C PRO I 1 N HYP I 2 1555 1555 1.33 LINK C HYP I 2 N GLY I 3 1555 1555 1.32 LINK C PRO I 4 N HYP I 5 1555 1555 1.32 LINK C HYP I 5 N GLY I 6 1555 1555 1.33 LINK C PRO I 7 N HYP I 8 1555 1555 1.32 LINK C HYP I 8 N GLY I 9 1555 1555 1.33 LINK C PRO I 22 N HYP I 23 1555 1555 1.32 LINK C HYP I 23 N GLY I 24 1555 1555 1.33 CRYST1 15.335 29.155 69.047 101.91 91.58 101.15 P 1 6 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 0.065210 0.012858 0.004690 0.00000 SCALE2 0.000000 0.034960 0.007730 0.00000 SCALE3 0.000000 0.000000 0.014838 0.00000