HEADER STRUCTURAL PROTEIN 05-AUG-24 9J1T TITLE STRUCTURE OF A TRIPLE-HELIX REGION OF HUMAN COLLAGEN TYPE IV FROM TITLE 2 TRAUTEC COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIPLE-HELIX REGION OF HUMAN COLLAGEN TYPE IV; 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 HUMAN COLLAGEN IV, TRIPLE-HELIX, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR X.FAN,Y.CHU,Y.ZHAI,S.FU,D.LI,P.FENG,K.CAO,X.WU,H.CAI,H.WANG,S.QIAN REVDAT 1 21-AUG-24 9J1T 0 JRNL AUTH X.FAN,Y.CHU,Y.ZHAI,S.FU,D.LI,P.FENG,K.CAO,X.WU,H.CAI,H.WANG, JRNL AUTH 2 S.QIAN JRNL TITL STRUCTURE OF A TRIPLE-HELIX REGION OF HUMAN COLLAGEN TYPE IV JRNL TITL 2 FROM TRAUTEC JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 11707 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.536 REMARK 3 FREE R VALUE TEST SET COUNT : 531 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 811 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.1910 REMARK 3 BIN FREE R VALUE SET COUNT : 37 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 481 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 125 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.61200 REMARK 3 B22 (A**2) : -0.80200 REMARK 3 B33 (A**2) : 1.45600 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.39500 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.076 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.077 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.033 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 524 ; 0.011 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 432 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 732 ; 1.849 ; 1.907 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1064 ; 0.569 ; 1.685 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 70 ; 5.916 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 3 ; 4.277 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 38 ;10.646 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 62 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 598 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 66 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 176 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 33 ; 0.139 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 272 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 72 ; 0.198 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 283 ; 2.037 ; 1.891 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 283 ; 2.037 ; 1.891 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 349 ; 3.236 ; 3.330 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 350 ; 3.233 ; 3.342 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 241 ; 2.124 ; 1.999 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 242 ; 2.120 ; 2.002 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 382 ; 3.102 ; 3.696 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 383 ; 3.098 ; 3.697 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 3 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 3 A 23 NULL REMARK 3 1 A 3 A 23 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 2 A 3 A 24 NULL REMARK 3 2 A 3 A 24 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 NCS GROUP NUMBER : 3 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 3 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 3 A 3 A 23 NULL REMARK 3 3 A 3 A 23 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9J1T COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 08-AUG-24. REMARK 100 THE DEPOSITION ID IS D_1300049621. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-24 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 : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99999 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11714 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 32.280 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 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 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: PHASER REMARK 200 STARTING MODEL: 1K6F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTAL-C4:0.2M NAAC, 0.1M SODIUM REMARK 280 CACODYLATE PH6.5, 30% PEG8,000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 8.85850 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: 4880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 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 PRO A 1 REMARK 465 HYP A 2 REMARK 465 PRO B 1 REMARK 465 PRO B 25 REMARK 465 HYP B 26 REMARK 465 GLY B 27 REMARK 465 PRO C 1 REMARK 465 HYP C 2 REMARK 465 HYP C 26 REMARK 465 GLY C 27 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 A 125 O HOH C 112 2.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 9J1T A 1 27 PDB 9J1T 9J1T 1 27 DBREF 9J1T B 1 27 PDB 9J1T 9J1T 1 27 DBREF 9J1T C 1 27 PDB 9J1T 9J1T 1 27 SEQRES 1 A 27 PRO HYP GLY PRO HYP GLY PRO HYP GLY GLU LYS GLY GLU SEQRES 2 A 27 ARG GLY TYR PRO GLY PRO HYP GLY PRO HYP GLY PRO HYP SEQRES 3 A 27 GLY SEQRES 1 B 27 PRO HYP GLY PRO HYP GLY PRO HYP GLY GLU LYS GLY GLU SEQRES 2 B 27 ARG GLY TYR PRO GLY PRO HYP GLY PRO HYP GLY PRO HYP SEQRES 3 B 27 GLY SEQRES 1 C 27 PRO HYP GLY PRO HYP GLY PRO HYP GLY GLU LYS GLY GLU SEQRES 2 C 27 ARG GLY TYR PRO GLY PRO HYP GLY PRO HYP GLY PRO HYP SEQRES 3 C 27 GLY HET HYP A 5 8 HET HYP A 8 8 HET HYP A 20 8 HET HYP A 23 8 HET HYP A 26 8 HET HYP B 2 8 HET HYP B 5 8 HET HYP B 8 8 HET HYP B 20 8 HET HYP B 23 8 HET HYP C 5 8 HET HYP C 8 8 HET HYP C 20 8 HET HYP C 23 8 HET GOL B 101 6 HETNAM HYP 4-HYDROXYPROLINE HETNAM GOL GLYCEROL HETSYN HYP HYDROXYPROLINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 HYP 14(C5 H9 N O3) FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *125(H2 O) LINK C PRO A 4 N HYP A 5 1555 1555 1.35 LINK C HYP A 5 N GLY A 6 1555 1555 1.33 LINK C PRO A 7 N HYP A 8 1555 1555 1.35 LINK C HYP A 8 N GLY A 9 1555 1555 1.33 LINK C PRO A 19 N HYP A 20 1555 1555 1.34 LINK C HYP A 20 N GLY A 21 1555 1555 1.32 LINK C PRO A 22 N HYP A 23 1555 1555 1.35 LINK C HYP A 23 N GLY A 24 1555 1555 1.33 LINK C PRO A 25 N HYP A 26 1555 1555 1.36 LINK C HYP A 26 N GLY A 27 1555 1555 1.34 LINK C HYP B 2 N GLY B 3 1555 1555 1.33 LINK C PRO B 4 N HYP B 5 1555 1555 1.34 LINK C HYP B 5 N GLY B 6 1555 1555 1.34 LINK C PRO B 7 N HYP B 8 1555 1555 1.35 LINK C HYP B 8 N GLY B 9 1555 1555 1.33 LINK C PRO B 19 N HYP B 20 1555 1555 1.35 LINK C HYP B 20 N GLY B 21 1555 1555 1.33 LINK C PRO B 22 N HYP B 23 1555 1555 1.35 LINK C HYP B 23 N GLY B 24 1555 1555 1.34 LINK C PRO C 4 N HYP C 5 1555 1555 1.34 LINK C HYP C 5 N GLY C 6 1555 1555 1.33 LINK C PRO C 7 N HYP C 8 1555 1555 1.35 LINK C HYP C 8 N GLY C 9 1555 1555 1.33 LINK C PRO C 19 N HYP C 20 1555 1555 1.34 LINK C HYP C 20 N GLY C 21 1555 1555 1.33 LINK C PRO C 22 N HYP C 23 1555 1555 1.34 LINK C HYP C 23 N GLY C 24 1555 1555 1.33 CRYST1 29.316 17.717 65.821 90.00 101.19 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 0.034111 0.000000 0.006750 0.00000 SCALE2 0.000000 0.056443 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015487 0.00000