HEADER STRUCTURAL PROTEIN 03-JUN-21 7F01 TITLE STRUCTURE OF A TRIPLE-HELIX REGION OF HUMAN COLLAGEN TYPE XVII COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLLAGEN TYPE XVII; COMPND 3 CHAIN: A, B, C; COMPND 4 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 KEYWDS COLLAGEN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.ZHU,X.YANG,F.SUN REVDAT 2 29-NOV-23 7F01 1 REMARK REVDAT 1 08-JUN-22 7F01 0 JRNL AUTH Y.ZHU,X.YANG,F.SUN JRNL TITL STRUCTURE OF A TRIPLE-HELIX REGION OF HUMAN COLLAGEN TYPE JRNL TITL 2 XVII JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 7168 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 719 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 1.6880 - 1.6300 0.95 684 69 0.2777 0.2927 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.87 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1 THROUGH 28) REMARK 3 ORIGIN FOR THE GROUP (A): -9.6130 -0.3449 25.0568 REMARK 3 T TENSOR REMARK 3 T11: 0.1217 T22: 0.0742 REMARK 3 T33: 0.0959 T12: -0.0008 REMARK 3 T13: 0.0096 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 0.5775 L22: 0.5448 REMARK 3 L33: 2.2265 L12: 0.0597 REMARK 3 L13: 0.8788 L23: 0.1947 REMARK 3 S TENSOR REMARK 3 S11: 0.0997 S12: -0.0373 S13: -0.0667 REMARK 3 S21: -0.1482 S22: 0.0070 S23: 0.0682 REMARK 3 S31: 0.0946 S32: -0.1205 S33: -0.0189 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN 'B' AND RESID 1 THROUGH 28) REMARK 3 ORIGIN FOR THE GROUP (A): -8.5029 0.5804 28.1979 REMARK 3 T TENSOR REMARK 3 T11: 0.0549 T22: 0.0959 REMARK 3 T33: 0.0802 T12: 0.0085 REMARK 3 T13: 0.0107 T23: 0.0023 REMARK 3 L TENSOR REMARK 3 L11: 0.7877 L22: 0.7256 REMARK 3 L33: 3.0630 L12: -0.0116 REMARK 3 L13: 1.3770 L23: -0.0107 REMARK 3 S TENSOR REMARK 3 S11: -0.0232 S12: 0.0583 S13: 0.1128 REMARK 3 S21: -0.0981 S22: -0.1460 S23: 0.0503 REMARK 3 S31: 0.0906 S32: 0.0707 S33: -0.0203 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN 'C' AND RESID 1 THROUGH 28) REMARK 3 ORIGIN FOR THE GROUP (A): -6.5357 0.4622 30.0285 REMARK 3 T TENSOR REMARK 3 T11: 0.0307 T22: 0.0316 REMARK 3 T33: 0.0831 T12: -0.0123 REMARK 3 T13: 0.0041 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 0.3387 L22: 0.6656 REMARK 3 L33: 1.0774 L12: 0.1026 REMARK 3 L13: 0.0992 L23: 0.1166 REMARK 3 S TENSOR REMARK 3 S11: -0.1318 S12: 0.0625 S13: 0.1114 REMARK 3 S21: -0.1108 S22: 0.0820 S23: 0.0848 REMARK 3 S31: -0.0310 S32: 0.1379 S33: -0.1829 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 7F01 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUN-21. REMARK 100 THE DEPOSITION ID IS D_1300022597. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF 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 : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7196 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.628 REMARK 200 RESOLUTION RANGE LOW (A) : 33.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : 0.41600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: 2WUH REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M POTASSIUM SODIUM TARTRATE, 0.1 M REMARK 280 CHES/ SODIUM HYDROXIDE PH 9.5, 0.2 M LITHIUM SULFATE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 10.63000 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: 5960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ACE A 1 REMARK 475 ACE B 1 REMARK 475 ACE C 1 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 C 114 O HOH C 128 1.90 REMARK 500 NH2 ARG B 11 O HOH B 201 2.01 REMARK 500 OD1 HYP C 3 O HOH C 101 2.11 REMARK 500 O HOH B 215 O HOH B 234 2.13 REMARK 500 NH1 ARG A 18 O HOH A 101 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 134 O HOH C 108 2546 1.90 REMARK 500 O HOH A 123 O HOH B 234 2446 2.15 REMARK 500 O HOH A 133 O HOH B 234 1545 2.16 REMARK 500 O HOH A 130 O HOH C 135 1455 2.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 7F01 A 1 29 PDB 7F01 7F01 1 29 DBREF 7F01 B 1 29 PDB 7F01 7F01 1 29 DBREF 7F01 C 1 29 PDB 7F01 7F01 1 29 SEQRES 1 A 29 ACE PRO HYP GLY PRO HYP GLY GLN ARG GLY ARG GLU GLY SEQRES 2 A 29 PRO MET GLY PRO ARG GLY PRO HYP GLY PRO HYP GLY PRO SEQRES 3 A 29 HYP GLY NH2 SEQRES 1 B 29 ACE PRO HYP GLY PRO HYP GLY GLN ARG GLY ARG GLU GLY SEQRES 2 B 29 PRO MET GLY PRO ARG GLY PRO HYP GLY PRO HYP GLY PRO SEQRES 3 B 29 HYP GLY NH2 SEQRES 1 C 29 ACE PRO HYP GLY PRO HYP GLY GLN ARG GLY ARG GLU GLY SEQRES 2 C 29 PRO MET GLY PRO ARG GLY PRO HYP GLY PRO HYP GLY PRO SEQRES 3 C 29 HYP GLY NH2 HET ACE A 1 3 HET HYP A 3 8 HET HYP A 6 8 HET HYP A 21 8 HET HYP A 24 8 HET HYP A 27 8 HET NH2 A 29 1 HET ACE B 1 3 HET HYP B 3 8 HET HYP B 6 8 HET HYP B 21 8 HET HYP B 24 8 HET HYP B 27 8 HET NH2 B 29 1 HET ACE C 1 3 HET HYP C 3 8 HET HYP C 6 8 HET HYP C 21 8 HET HYP C 24 8 HET HYP C 27 8 HET NH2 C 29 1 HET SO4 B 101 5 HETNAM ACE ACETYL GROUP HETNAM HYP 4-HYDROXYPROLINE HETNAM NH2 AMINO GROUP HETNAM SO4 SULFATE ION HETSYN HYP HYDROXYPROLINE FORMUL 1 ACE 3(C2 H4 O) FORMUL 1 HYP 15(C5 H9 N O3) FORMUL 1 NH2 3(H2 N) FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *120(H2 O) LINK C ACE A 1 N PRO A 2 1555 1555 1.33 LINK C PRO A 2 N HYP A 3 1555 1555 1.33 LINK C HYP A 3 N GLY A 4 1555 1555 1.33 LINK C PRO A 5 N HYP A 6 1555 1555 1.33 LINK C HYP A 6 N GLY A 7 1555 1555 1.33 LINK C PRO A 20 N HYP A 21 1555 1555 1.33 LINK C HYP A 21 N GLY A 22 1555 1555 1.33 LINK C PRO A 23 N HYP A 24 1555 1555 1.33 LINK C HYP A 24 N GLY A 25 1555 1555 1.33 LINK C PRO A 26 N HYP A 27 1555 1555 1.33 LINK C HYP A 27 N GLY A 28 1555 1555 1.33 LINK C GLY A 28 N NH2 A 29 1555 1555 1.33 LINK C ACE B 1 N PRO B 2 1555 1555 1.33 LINK C PRO B 2 N HYP B 3 1555 1555 1.33 LINK C HYP B 3 N GLY B 4 1555 1555 1.33 LINK C PRO B 5 N HYP B 6 1555 1555 1.33 LINK C HYP B 6 N GLY B 7 1555 1555 1.33 LINK C PRO B 20 N HYP B 21 1555 1555 1.33 LINK C HYP B 21 N GLY B 22 1555 1555 1.33 LINK C PRO 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 PRO B 26 N HYP B 27 1555 1555 1.33 LINK C HYP B 27 N GLY B 28 1555 1555 1.33 LINK C GLY B 28 N NH2 B 29 1555 1555 1.33 LINK C ACE C 1 N PRO C 2 1555 1555 1.33 LINK C PRO C 2 N HYP C 3 1555 1555 1.33 LINK C HYP C 3 N GLY C 4 1555 1555 1.33 LINK C PRO C 5 N HYP C 6 1555 1555 1.33 LINK C HYP C 6 N GLY C 7 1555 1555 1.32 LINK C PRO C 20 N HYP C 21 1555 1555 1.33 LINK C HYP C 21 N GLY C 22 1555 1555 1.33 LINK C PRO C 23 N HYP C 24 1555 1555 1.33 LINK C HYP C 24 N GLY C 25 1555 1555 1.33 LINK C PRO C 26 N HYP C 27 1555 1555 1.33 LINK C HYP C 27 N GLY C 28 1555 1555 1.33 LINK C GLY C 28 N NH2 C 29 1555 1555 1.33 CRYST1 20.320 21.260 67.600 90.00 90.38 90.00 P 1 21 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 0.049213 0.000000 0.000326 0.00000 SCALE2 0.000000 0.047037 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014793 0.00000 HETATM 1 C ACE A 1 10.567 -0.025 57.178 0.00 15.16 C ANISOU 1 C ACE A 1 1896 2067 1795 -7 -59 -185 C HETATM 2 O ACE A 1 10.796 1.040 56.606 0.00 16.60 O ANISOU 2 O ACE A 1 2022 2292 1995 -26 0 -209 O HETATM 3 CH3 ACE A 1 10.420 -0.096 58.673 0.00 17.10 C ANISOU 3 CH3 ACE A 1 2196 2301 2001 -33 -91 -156 C