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- PDB-6qv7: Crystal structure of a CHAD domain from Chlorobium tepidum -

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Basic information

Entry
Database: PDB / ID: 6qv7
TitleCrystal structure of a CHAD domain from Chlorobium tepidum
ComponentsUncharacterized protein
KeywordsNUCLEAR PROTEIN / four-helix bundle / inorganic polyphosphate binding protein / all alpha-helical protein
Function / homology
Function and homology information


CHAD domain / CHAD domain / CHAD domain superfamily / CHAD / CHAD domain / CHAD domain / CHAD domain profile. / Alpha solenoid / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / CHAD domain-containing protein
Similarity search - Component
Biological speciesChlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsLorenzo-Orts, L. / Hothorn, M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
European Research Council310856 Switzerland
CitationJournal: Life Sci Alliance / Year: 2019
Title: Molecular characterization of CHAD domains as inorganic polyphosphate-binding modules.
Authors: Lorenzo-Orts, L. / Hohmann, U. / Zhu, J. / Hothorn, M.
History
DepositionMar 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,75121
Polymers36,2491
Non-polymers1,50120
Water3,225179
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,00384
Polymers144,9974
Non-polymers6,00680
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area24620 Å2
ΔGint-413 kcal/mol
Surface area55470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.483, 95.735, 102.779
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-718-

HOH

21A-739-

HOH

31A-801-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 36249.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Strain: ATCC 49652 / DSM 12025 / NBRC 103806 / TLS / Gene: CT0884 / Plasmid: pMH-HT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8KE09
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2 M (NH4)2SO4, 5 % isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.977948 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977948 Å / Relative weight: 1
ReflectionResolution: 1.72→36.805 Å / Num. obs: 70380 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 39.3 Å2 / CC1/2: 1 / Rrim(I) all: 0.074 / Rsym value: 0.069 / Net I/σ(I): 16.1
Reflection shellResolution: 1.72→1.82 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 11411 / CC1/2: 0.5 / Rrim(I) all: 2.21 / Rsym value: 2.05 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3e0s

3e0s


Resolution: 1.72→36.805 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.79
RfactorNum. reflection% reflection
Rfree0.2218 3510 4.99 %
Rwork0.1887 --
obs0.1903 70305 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.72→36.805 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 0 88 179 2800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012707
X-RAY DIFFRACTIONf_angle_d1.0713646
X-RAY DIFFRACTIONf_dihedral_angle_d10.5892254
X-RAY DIFFRACTIONf_chiral_restr0.064398
X-RAY DIFFRACTIONf_plane_restr0.008468
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7199-1.74340.40971420.41032691X-RAY DIFFRACTION99
1.7434-1.76830.4041360.38812610X-RAY DIFFRACTION100
1.7683-1.79470.31051410.36682694X-RAY DIFFRACTION100
1.7947-1.82280.40231400.3312685X-RAY DIFFRACTION100
1.8228-1.85270.41081370.30332652X-RAY DIFFRACTION100
1.8527-1.88460.3551360.29842655X-RAY DIFFRACTION100
1.8846-1.91890.30311390.28842682X-RAY DIFFRACTION100
1.9189-1.95580.30611420.27582669X-RAY DIFFRACTION100
1.9558-1.99570.30211440.26262676X-RAY DIFFRACTION100
1.9957-2.03910.26171390.23712655X-RAY DIFFRACTION100
2.0391-2.08650.27461420.21772659X-RAY DIFFRACTION100
2.0865-2.13870.24251410.20062670X-RAY DIFFRACTION100
2.1387-2.19650.24431440.1882694X-RAY DIFFRACTION100
2.1965-2.26110.22271430.1862672X-RAY DIFFRACTION100
2.2611-2.33410.2341460.18442675X-RAY DIFFRACTION100
2.3341-2.41750.24871430.18022665X-RAY DIFFRACTION100
2.4175-2.51430.20821360.17972685X-RAY DIFFRACTION100
2.5143-2.62870.25451420.1882678X-RAY DIFFRACTION100
2.6287-2.76720.23131410.18552634X-RAY DIFFRACTION100
2.7672-2.94050.20081430.18192685X-RAY DIFFRACTION100
2.9405-3.16750.21211440.17872680X-RAY DIFFRACTION100
3.1675-3.4860.18651430.17392683X-RAY DIFFRACTION100
3.486-3.98990.1941370.15942664X-RAY DIFFRACTION100
3.9899-5.02490.14961360.15012691X-RAY DIFFRACTION100
5.0249-36.81320.24691330.18992691X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.1163-0.769-4.38077.4839-0.7244.9426-0.7341.2461-1.53840.1969-0.05260.80880.5819-1.90810.66130.5095-0.03750.03050.8083-0.1080.515215.0073-2.81849.9511
24.938-2.8233-2.73093.53361.35122.98510.08170.5798-0.2402-0.0604-0.19640.2972-0.2407-0.44020.14740.3049-0.0188-0.01760.2909-0.02040.255711.601810.486814.8123
35.3527-1.7283-6.7750.55971.64347.41310.492-0.20950.7185-0.08090.0264-0.1066-0.63530.1341-0.47830.37150.0194-0.00340.28540.00570.323712.182718.468722.1692
43.58850.0525-3.9062.0308-0.78624.00180.23040.3860.2122-0.16310.1160.074-0.3151-0.4888-0.38780.32130.0109-0.03220.2938-0.02340.3318-4.292420.699434.0273
59.6567-7.0389-1.27426.07450.4452.10210.11490.31150.42040.0662-0.1327-0.2163-0.2241-0.1551-0.0310.325-0.0051-0.00880.30410.01170.268821.785514.27846.9587
61.953-0.7238-1.82232.9035-0.74472.4442-0.0712-0.4048-0.08830.21520.222-0.2903-0.0661.4116-0.15040.26680.0334-0.00220.4661-0.010.373626.5822-3.976626.3442
73.10710.0509-2.36556.58955.15557.67540.0093-0.1491-0.14410.33910.0456-0.15570.18090.1525-0.08750.20140.04080.01150.25680.05280.304316.9881-2.67327.7389
84.0097-4.9528-2.87258.36594.17964.7351-0.1086-0.07020.11870.24280.1015-0.26530.15140.08040.00820.1836-0.0318-0.00850.19280.01260.20936.96279.984243.1185
96.638-0.1454-2.08129.26340.29582.0539-0.9885-0.3117-0.9537-0.01990.2133-0.33931.86940.54180.79990.57260.14780.09080.40610.00860.517922.1544-14.600824.869
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 207 through 220 )
2X-RAY DIFFRACTION2chain 'A' and (resid 221 through 274 )
3X-RAY DIFFRACTION3chain 'A' and (resid 275 through 303 )
4X-RAY DIFFRACTION4chain 'A' and (resid 304 through 342 )
5X-RAY DIFFRACTION5chain 'A' and (resid 343 through 375 )
6X-RAY DIFFRACTION6chain 'A' and (resid 376 through 397 )
7X-RAY DIFFRACTION7chain 'A' and (resid 398 through 440 )
8X-RAY DIFFRACTION8chain 'A' and (resid 441 through 505 )
9X-RAY DIFFRACTION9chain 'A' and (resid 506 through 522 )

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