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- PDB-4ilu: Crystal structure of Mycobacterium tuberculosis CarD -

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Basic information

Entry
Database: PDB / ID: 4ilu
TitleCrystal structure of Mycobacterium tuberculosis CarD
ComponentsRNA polymerase-binding transcription factor CarD
KeywordsTRANSCRIPTION / Tudor like domain / five helical fold / RNA polymerase binding / Transcription regulation
Function / homology
Function and homology information


regulation of growth rate / stringent response / rRNA transcription
Similarity search - Function
CarD-like, C-terminal domain / : / CarD, C-terminal / CarD-like, C-terminal domain / CarD-like/TRCF, RNAP-interacting domain / CarD-like/TRCF, RNAP-interacting domain superfamily / CarD-like/TRCF RID domain / CarD-like/TRCF domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase-binding transcription factor CarD / RNA polymerase-binding transcription factor CarD
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.3 Å
AuthorsThakur, K.G. / Kaur, G.
CitationJournal: Proteins / Year: 2014
Title: Crystal structure of Mycobacterium tuberculosis CarD, an essential RNA polymerase binding protein, reveals a quasidomain-swapped dimeric structural architecture.
Authors: Kaur, G. / Dutta, D. / Thakur, K.G.
History
DepositionJan 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase-binding transcription factor CarD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6618
Polymers18,9891
Non-polymers6727
Water1,35175
1
A: RNA polymerase-binding transcription factor CarD
hetero molecules

A: RNA polymerase-binding transcription factor CarD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,32216
Polymers37,9772
Non-polymers1,34514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7980 Å2
ΔGint-193 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.500, 93.500, 86.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RNA polymerase-binding transcription factor CarD


Mass: 18988.516 Da / Num. of mol.: 1 / Mutation: S162A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: carD, MT3689, Rv3583c / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: O53568, UniProt: P9WJG3*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 4.98 Å3/Da / Density % sol: 75.29 % / Mosaicity: 0.64 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.5M Lithium sulphate, 0.1M HEPES pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→93.5 Å / Num. all: 17652 / Num. obs: 17652 / % possible obs: 100 % / Redundancy: 11.4 % / Rsym value: 0.076 / Net I/σ(I): 18.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.4211.30.5550.5291.32852325210.1640.5550.5294.8100
2.42-2.5711.60.3620.3462.12757523870.1050.3620.3466.1100
2.57-2.7511.40.2890.2752.52553222460.0850.2890.2758.5100
2.75-2.9711.50.1640.1574.42417620940.0480.1640.15713100
2.97-3.2511.50.1060.1016.82260119580.0310.1060.10118.5100
3.25-3.6411.50.0710.0664.92052917800.0220.0710.06627.2100
3.64-4.211.30.0580.05610.41776615680.0170.0580.05635.1100
4.2-5.1411.40.0570.05411.11563113660.0160.0570.05438.8100
5.14-7.2711.20.0380.03715.71210910810.0110.0380.03735.4100
7.27-43.25510.10.0360.0341365616510.0110.0360.03440.899.6

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.20data scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→41.814 Å / Occupancy max: 1 / Occupancy min: 0.64 / FOM work R set: 0.8366 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2327 892 5.07 %RANDOM
Rwork0.2072 ---
obs0.2085 17585 99.88 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.229 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 123.79 Å2 / Biso mean: 50.4053 Å2 / Biso min: 22.61 Å2
Baniso -1Baniso -2Baniso -3
1--4.2997 Å2-0 Å20 Å2
2---4.2997 Å20 Å2
3---8.5994 Å2
Refinement stepCycle: LAST / Resolution: 2.3→41.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1298 0 35 75 1408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031347
X-RAY DIFFRACTIONf_angle_d0.6951825
X-RAY DIFFRACTIONf_chiral_restr0.047203
X-RAY DIFFRACTIONf_plane_restr0.003232
X-RAY DIFFRACTIONf_dihedral_angle_d17.356489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.44410.27631550.264627212876
2.4441-2.63280.26761520.255127152867
2.6328-2.89770.29611370.246927652902
2.8977-3.31680.24891600.220427372897
3.3168-4.17830.21311440.178227922936
4.1783-41.82140.20341440.192329633107
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)
12.804-0.95660.4151.1157-0.42392.7614-0.17880.21910.087-0.0907-0.16920.0539-0.2672-0.49080.52640.2472-0.0241-0.00880.3207-0.00740.259512.590922.53880.2225
21.83542.84230.29135.8077-1.47527.1952-0.24770.0211-0.26160.54790.1831-0.14830.3718-0.1933-0.10160.4465-0.0179-0.06020.206-0.0630.258311.24329.26216.7744
35.9113-6.1304-0.6837.1639-1.08964.1137-0.2335-0.2506-0.04040.64030.2686-0.0731-0.3126-0.2167-0.13810.3718-0.0647-0.01460.29380.00250.224817.858217.835311.9769
41.3355-0.96681.00376.5045-2.48413.72570.0422-0.0029-0.09940.3807-0.2449-1.14890.27240.45770.12090.2717-0.0668-0.10490.32770.05870.420334.85380.683614.408
52.876-2.08790.79886.6248-1.16313.68150.0583-0.3511-0.3240.11320.12040.47980.1391-0.2257-0.13550.2702-0.0656-0.03320.26070.07330.284722.63772.544110.8418
64.98255.5121-4.48496.2128-4.65814.93260.04930.1061.03420.24270.61240.5459-0.12740.4854-0.3910.3028-0.01640.05940.42920.02760.346631.990316.6585-0.4532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:30)A2 - 30
2X-RAY DIFFRACTION2chain 'A' and (resseq 31:49)A31 - 49
3X-RAY DIFFRACTION3chain 'A' and (resseq 50:74)A50 - 74
4X-RAY DIFFRACTION4chain 'A' and (resseq 75:100)A75 - 100
5X-RAY DIFFRACTION5chain 'A' and (resseq 101:163)A101 - 163
6X-RAY DIFFRACTION6chain 'A' and (resseq 164:170)A164 - 170

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