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- PDB-6cz6: Mycobacterium tuberculosis transcriptional regulator -

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Basic information

Entry
Database: PDB / ID: 6cz6
TitleMycobacterium tuberculosis transcriptional regulator
ComponentsHTH-type transcriptional regulator PrpR
KeywordsTRANSCRIPTION / regulator / DNA BINDING PROTEIN
Function / homology
Function and homology information


propionate metabolic process, methylcitrate cycle / cholesterol metabolic process / response to hypoxia / DNA-binding transcription factor activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Short-chain fatty acyl coenzyme A regulators, C-terminal / HTH-type transcriptional regulator RamB / Short-chain fatty acyl coenzyme A regulator, C-terminal / IrrE N-terminal-like domain / IrrE N-terminal-like domain / : / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily
Similarity search - Domain/homology
COENZYME A / IRON/SULFUR CLUSTER / HTH-type transcriptional regulator PrpR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsTang, S. / Sacchettini, J.
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Structural and functional insight into the Mycobacterium tuberculosis protein PrpR reveals a novel type of transcription factor.
Authors: Tang, S. / Hicks, N.D. / Cheng, Y.S. / Silva, A. / Fortune, S.M. / Sacchettini, J.C.
History
DepositionApr 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulator PrpR
B: HTH-type transcriptional regulator PrpR
C: HTH-type transcriptional regulator PrpR
D: HTH-type transcriptional regulator PrpR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,72812
Polymers192,2514
Non-polymers4,4778
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23340 Å2
ΔGint-146 kcal/mol
Surface area49540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.188, 142.365, 145.963
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 153 through 465 or resid 468 through 480))
21(chain B and (resid 153 through 465 or resid 468 through 480))
31(chain C and (resid 153 through 465 or resid 468 through 480))
41chain D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSEGLYGLY(chain A and (resid 153 through 465 or resid 468 through 480))AA153 - 46596 - 408
12ALAALASERSER(chain A and (resid 153 through 465 or resid 468 through 480))AA468 - 480411 - 423
21MSEMSEGLYGLY(chain B and (resid 153 through 465 or resid 468 through 480))BB153 - 46596 - 408
22ALAALASERSER(chain B and (resid 153 through 465 or resid 468 through 480))BB468 - 480411 - 423
31MSEMSEGLYGLY(chain C and (resid 153 through 465 or resid 468 through 480))CC153 - 46596 - 408
32ALAALASERSER(chain C and (resid 153 through 465 or resid 468 through 480))CC468 - 480411 - 423
41MSEMSESERSERchain DDD153 - 48096 - 423

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Components

#1: Protein
HTH-type transcriptional regulator PrpR / Propionate regulator / PRPR


Mass: 48062.824 Da / Num. of mol.: 4 / Fragment: residues 81-486
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25618 / H37Rv / Gene: prpR, Rv1129c, RVBD_1129c, P425_01178 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O06581
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: Bicine pH 9.5, Sodium Acetate, Zwittergent 3-14 / PH range: 7.5-9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 2, 2015
RadiationMonochromator: Si(111) Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 55505 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 65.88 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.043 / Rrim(I) all: 0.117 / Χ2: 1.45 / Net I/σ(I): 6.9 / Num. measured all: 412165
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.757.41.13227470.7180.4461.2170.538100
2.75-2.87.40.9827370.7930.3851.0540.535100
2.8-2.857.50.79127380.8390.310.850.544100
2.85-2.917.50.69627610.8850.2730.7480.564100
2.91-2.977.50.55527220.9210.2170.5960.553100
2.97-3.047.50.42827310.9440.1680.460.598100
3.04-3.127.50.34927550.9620.1360.3750.615100
3.12-3.27.50.28727420.9730.1120.3080.637100
3.2-3.37.50.21727560.9840.0850.2330.677100
3.3-3.47.50.17827350.9880.0690.1910.773100
3.4-3.527.50.15827670.9890.0620.170.847100
3.52-3.667.50.12127490.9940.0470.130.973100
3.66-3.837.50.09927830.9950.0390.1071.037100
3.83-4.037.50.08627390.9970.0330.0921.17199.9
4.03-4.297.40.07727930.9960.030.0831.44899.9
4.29-4.627.40.07527830.9960.030.0811.93899.7
4.62-5.087.30.08627970.9940.0340.0932.89100
5.08-5.817.40.08228210.9960.0320.0882.972100
5.81-7.327.30.07828620.9970.030.0833.879100
7.32-506.90.05929870.9980.0240.0645.88299.7

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Processing

Software
NameVersionClassification
PHENIX1.13rc1_2954refinement
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
SHELXphasing
BUCCANEERmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.7→45.678 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.212 2894 5.22 %Random selection
Rwork0.1819 52533 --
obs0.1835 55427 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.51 Å2 / Biso mean: 67.5606 Å2 / Biso min: 31.89 Å2
Refinement stepCycle: final / Resolution: 2.7→45.678 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10267 0 352 24 10643
Biso mean--76.69 52 -
Num. residues----1309
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A6102X-RAY DIFFRACTION8.577TORSIONAL
12B6102X-RAY DIFFRACTION8.577TORSIONAL
13C6102X-RAY DIFFRACTION8.577TORSIONAL
14D6102X-RAY DIFFRACTION8.577TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6996-2.74390.32691300.30642196232688
2.7439-2.79120.36371230.298924712594100
2.7912-2.84190.28761200.285725002620100
2.8419-2.89660.31420.252424792621100
2.8966-2.95570.26121490.261524902639100
2.9557-3.020.31011440.248724772621100
3.02-3.09020.30951330.252424922625100
3.0902-3.16750.25171300.250124922622100
3.1675-3.25310.29721220.239724932615100
3.2531-3.34880.29641250.239325112636100
3.3488-3.45680.27621380.225625172655100
3.4568-3.58030.27561490.216924932642100
3.5803-3.72360.23791390.183125042643100
3.7236-3.8930.23791490.174525002649100
3.893-4.09810.16271460.155424962642100
4.0981-4.35470.18181480.144225162664100
4.3547-4.69060.15051290.129825152644100
4.6906-5.16210.1581310.13525532684100
5.1621-5.90770.21521440.151325632707100
5.9077-7.43780.18131520.171525782730100
7.4378-45.68480.15521510.15526972848100
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)
14.35282.3313-1.34673.8248-0.34713.2070.05230.62690.0814-0.50740.11870.2371-0.0235-0.1075-0.23880.74280.0723-0.13290.68910.02390.62120.097216.72735.5026
21.31730.12160.09234.25360.11931.6630.08510.28180.0117-0.32290.0280.18050.0864-0.1193-0.13220.4483-0.0017-0.02510.4297-0.00540.36682.530716.699310.6218
31.6298-1.7867-0.71563.543-0.4743.32480.0151-0.10940.1057-0.01680.24770.57230.5873-0.223-0.25310.7547-0.0151-0.07770.5463-0.03620.6144-1.2761-1.374823.9034
41.708-0.3064-1.03510.4364-0.39742.78930.0606-0.0097-0.1829-0.02010.0876-0.25570.5468-0.0828-0.11590.6430.0348-0.12140.4606-0.05530.48985.3575-2.496222.3134
50.9577-0.0111-1.5261.9456-1.02722.99070.0420.2745-0.6273-0.13240.10190.72430.2153-0.2068-0.1890.818-0.1026-0.14760.77210.00450.8695-12.838-10.282333.7353
60.41510.28450.26110.19390.17760.1637-0.45120.24430.4472-0.89550.45720.75080.8838-0.61190.11940.7349-0.1857-0.20120.83510.12441.0008-15.9286-17.030144.4418
73.7142-1.96092.36293.6173-2.18515.26020.1488-0.2719-0.03120.38790.21140.4798-0.4041-0.5813-0.37930.60720.0870.1950.5996-0.00040.8378-17.191-3.82658.8267
89.2772.9268-3.1726.0183-2.33666.99660.2581-0.3773-0.65430.8194-0.1747-0.49660.6303-0.3016-0.13460.80780.00320.05510.79360.06640.6488-4.9579-20.41368.5349
91.97120.62-0.40483.3574-0.34831.41340.0962-0.20850.0030.37440.08390.34010.0197-0.2258-0.15270.5071-0.00870.09010.4896-0.00850.4612-9.225-11.537458.6517
101.62481.58540.80373.4817-0.82284.16550.06530.16830.26880.14540.20020.4316-0.5634-0.3057-0.25250.57190.02990.14190.4366-0.040.5356-3.4696.389445.4641
113.3108-1.1557-1.06224.29252.4765.79180.01490.1081-0.03990.3343-0.4590.9675-0.1396-0.12520.32210.49910.0061-0.02270.4154-0.01890.42920.6454-2.430647.0559
121.6276-0.78091.84682.9006-1.33635.1933-0.06370.15550.55610.29390.19660.298-0.8298-0.0018-0.1350.65730.02940.20640.4984-0.07120.6714-2.260217.273741.7731
130.47081.4327-1.2066.3735-6.00295.8273-0.0117-0.13190.13381.20410.79270.3897-1.0667-0.7139-0.80420.880.1290.17620.6740.06710.8487-5.855424.617422.2639
144.5834-2.20082.00116.0732-3.24884.94850.17560.02470.13390.5606-0.4365-0.6735-0.46970.71260.40930.5557-0.1258-0.06570.8444-0.02890.621541.418422.073731.6896
153.25371.3642-1.59753.11410.43147.81390.26170.39770.6235-0.6121-0.3371-0.264-0.62440.1824-0.09330.8067-0.06590.00030.7550.08890.837629.141331.045514.7724
164.79031.30430.67953.4275-1.91462.70170.20250.4562-0.0157-0.0727-0.19740.035-0.25340.123-0.02930.5947-0.03460.09980.6405-0.04930.446932.390817.789311.6742
174.2577-0.0872-0.31241.2643-0.14673.43460.0567-0.11690.38110.1924-0.2087-0.3143-0.52780.33450.10640.5239-0.1359-0.03150.44380.01850.490633.948923.881831.418
182.0553-0.2253-1.82964.1981-1.08143.896-0.1418-0.3391-0.54740.3837-0.1207-0.220.10520.66540.23640.5344-0.069-0.02270.5756-0.07830.452827.87688.230240.8947
192.01840.84920.61293.6107-0.16020.34310.1837-0.1969-0.08330.3762-0.10770.0589-0.22990.54440.01020.6352-0.0832-0.00320.5602-0.07160.472323.286712.45243.2711
202.1243.0456-1.58034.758-2.40171.22170.1558-0.4299-0.10130.7466-0.3856-0.4515-0.40690.29950.33930.7508-0.0636-0.09410.88340.03460.647731.3567-7.209557.2648
215.2391.0575-0.76411.8971-0.0691.73480.3060.1543-0.3133-0.2388-0.2542-0.2540.14450.2410.12480.78110.1843-0.01840.6973-0.05430.713930.9704-28.432249.4845
226.4543-0.84382.47579.04840.86719.34780.3591-0.8499-0.49681.1067-0.59180.27030.7405-0.44780.25520.7742-0.1032-0.00720.65820.02540.696512.0902-32.8561.5164
235.81010.77930.53944.7656-2.55966.11940.2059-0.8545-0.13990.4158-0.40060.1693-0.01510.18350.14060.3623-0.0304-0.04550.4605-0.0260.303418.8444-20.638169.8769
241.96950.1632-0.23371.13970.18953.39010.08280.0395-0.3276-0.2263-0.1637-0.0660.43170.12030.04120.58380.0797-0.0150.423-0.00890.531922.1474-26.522650.8767
252.29060.75041.46053.67070.32045.0435-0.16150.05390.1298-0.6801-0.0089-0.3243-0.1270.56420.22330.68260.06440.01060.5534-0.0140.509526.3327-12.339135.6032
262.5855-2.6581-1.69737.35294.95.11150.1311-0.44060.4152-0.26810.2181-0.34630.0670.5731-0.20870.5944-0.0067-0.01010.5891-0.05910.68417.3342-8.116945.8667
271.76121.28260.14483.9813-1.67951.2227-0.0050.12030.0698-1.16310.0326-0.09160.32430.0299-0.02120.85590.1285-0.00290.539-0.09950.496620.1159-18.220728.003
280.3513-0.11250.24043.9482-2.7191.9468-0.12080.47910.0097-0.31730.3228-0.05340.52680.21060.42840.64020.13510.12880.809-0.02230.666237.7461.189623.429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 153 through 202 )A153 - 202
2X-RAY DIFFRACTION2chain 'A' and (resid 203 through 334 )A203 - 334
3X-RAY DIFFRACTION3chain 'A' and (resid 335 through 399 )A335 - 399
4X-RAY DIFFRACTION4chain 'A' and (resid 400 through 444 )A400 - 444
5X-RAY DIFFRACTION5chain 'A' and (resid 445 through 464 )A445 - 464
6X-RAY DIFFRACTION6chain 'A' and (resid 465 through 480 )A465 - 480
7X-RAY DIFFRACTION7chain 'B' and (resid 153 through 181 )B153 - 181
8X-RAY DIFFRACTION8chain 'B' and (resid 182 through 200 )B182 - 200
9X-RAY DIFFRACTION9chain 'B' and (resid 201 through 334 )B201 - 334
10X-RAY DIFFRACTION10chain 'B' and (resid 335 through 399 )B335 - 399
11X-RAY DIFFRACTION11chain 'B' and (resid 400 through 425 )B400 - 425
12X-RAY DIFFRACTION12chain 'B' and (resid 426 through 464 )B426 - 464
13X-RAY DIFFRACTION13chain 'B' and (resid 465 through 480 )B465 - 480
14X-RAY DIFFRACTION14chain 'C' and (resid 153 through 181 )C153 - 181
15X-RAY DIFFRACTION15chain 'C' and (resid 182 through 200 )C182 - 200
16X-RAY DIFFRACTION16chain 'C' and (resid 201 through 250 )C201 - 250
17X-RAY DIFFRACTION17chain 'C' and (resid 251 through 334 )C251 - 334
18X-RAY DIFFRACTION18chain 'C' and (resid 335 through 383 )C335 - 383
19X-RAY DIFFRACTION19chain 'C' and (resid 384 through 444 )C384 - 444
20X-RAY DIFFRACTION20chain 'C' and (resid 445 through 480 )C445 - 480
21X-RAY DIFFRACTION21chain 'D' and (resid 153 through 181 )D153 - 181
22X-RAY DIFFRACTION22chain 'D' and (resid 182 through 200 )D182 - 200
23X-RAY DIFFRACTION23chain 'D' and (resid 201 through 225 )D201 - 225
24X-RAY DIFFRACTION24chain 'D' and (resid 226 through 334 )D226 - 334
25X-RAY DIFFRACTION25chain 'D' and (resid 335 through 390 )D335 - 390
26X-RAY DIFFRACTION26chain 'D' and (resid 391 through 410 )D391 - 410
27X-RAY DIFFRACTION27chain 'D' and (resid 411 through 444 )D411 - 444
28X-RAY DIFFRACTION28chain 'D' and (resid 445 through 480 )D445 - 480

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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