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- PDB-4pcq: Crystal Structure of MtbAldR (Rv2779c) -

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Basic information

Entry
Database: PDB / ID: 4pcq
TitleCrystal Structure of MtbAldR (Rv2779c)
ComponentsPossible transcriptional regulatory protein (Probably Lrp/AsnC-family)
KeywordsTRANSCRIPTION / Lrp / AsnC / Feast/famine regulatory protein
Function / homology
Function and homology information


response to amino acid / Modulation by Mtb of host immune system / sequence-specific DNA binding / cytosol
Similarity search - Function
AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / AsnC-type HTH domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel ...AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / AsnC-type HTH domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Possible transcriptional regulatory protein (Probably Lrp/AsnC-family)
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsDey, A. / Ramachandran, R.
Funding support India, 3items
OrganizationGrant numberCountry
Council of Scientific and Industrial ResearchBSC0104 India
Department of BiotechnologyGAP0083 India
CSIR-Central Drug Research InstituteBSC0121 India
CitationJournal: To be published
Title: Crystal structure of MtbAldR
Authors: Dey, A. / Ramachandran, R.
History
DepositionApr 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Possible transcriptional regulatory protein (Probably Lrp/AsnC-family)
B: Possible transcriptional regulatory protein (Probably Lrp/AsnC-family)
C: Possible transcriptional regulatory protein (Probably Lrp/AsnC-family)
D: Possible transcriptional regulatory protein (Probably Lrp/AsnC-family)


Theoretical massNumber of molelcules
Total (without water)84,4564
Polymers84,4564
Non-polymers00
Water59433
1
A: Possible transcriptional regulatory protein (Probably Lrp/AsnC-family)
B: Possible transcriptional regulatory protein (Probably Lrp/AsnC-family)


Theoretical massNumber of molelcules
Total (without water)42,2282
Polymers42,2282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-22 kcal/mol
Surface area14820 Å2
MethodPISA
2
C: Possible transcriptional regulatory protein (Probably Lrp/AsnC-family)
D: Possible transcriptional regulatory protein (Probably Lrp/AsnC-family)


Theoretical massNumber of molelcules
Total (without water)42,2282
Polymers42,2282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-16 kcal/mol
Surface area15100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.739, 146.099, 49.961
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Possible transcriptional regulatory protein (Probably Lrp/AsnC-family) / Transcriptional regulator Lrp/AsnC-family


Mass: 21114.119 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: MtbAldR / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2779c, RVBD_2779c / Production host: Escherichia coli (E. coli) / References: UniProt: O33321
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.16 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2 M trisodium citrate dihydrate, 20% PEG 3350

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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: Apr 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.95→27.194 Å / Num. obs: 17732 / % possible obs: 99.5 % / Redundancy: 6 % / Net I/σ(I): 25.6
Reflection shellResolution: 2.95→3.02 Å / Redundancy: 5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.4 / % possible all: 93.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ivm

2ivm


Resolution: 2.95→27.19 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2992 844 5.31 %
Rwork0.2631 --
obs0.265 15881 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.95→27.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4221 0 0 33 4254
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054273
X-RAY DIFFRACTIONf_angle_d0.9535814
X-RAY DIFFRACTIONf_dihedral_angle_d14.2021462
X-RAY DIFFRACTIONf_chiral_restr0.062709
X-RAY DIFFRACTIONf_plane_restr0.004773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.13460.4061470.34032357X-RAY DIFFRACTION97
3.1346-3.37620.3361400.30752474X-RAY DIFFRACTION100
3.3762-3.71520.31591410.26942474X-RAY DIFFRACTION100
3.7152-4.2510.28881440.24362505X-RAY DIFFRACTION100
4.251-5.34920.23841310.21632561X-RAY DIFFRACTION100
5.3492-27.19560.27761410.26422666X-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)
13.156-0.86610.42670.5277-0.10870.8964-0.274-0.41910.2934-0.41390.32970.13511.0059-0.3696-0.0437-0.84170.08480.1160.55830.10031.258313.799628.74458.686
29.5326-3.3783-3.42435.7315-2.65444.53570.111.31390.5369-0.4924-0.22880.37840.3641-0.26750.12240.23820.01540.0660.7524-0.14860.767441.877832.11097.4748
34.15041.01710.17233.9745-1.16031.52140.0855-0.51090.17990.788-0.07030.0612-0.09540.1139-0.05230.36690.0547-0.07660.4603-0.09440.213242.335716.952920.2854
45.34611.5129-1.02652.6524-3.15432.0002-0.0155-0.129-0.1772-0.27530.32720.36080.7282-0.1954-0.3960.29130.145-0.11660.8125-0.01180.30248.231613.377612.9562
50.2431-1.0278-0.21854.1620.58912.0461-0.1650.05630.48320.1556-0.45330.75180.08690.30120.30980.37050.1221-0.0340.30570.00610.14233.852822.22120.7801
62.7159-0.31960.22893.8291-0.37670.8769-0.2806-0.2403-0.18150.6784-0.6268-0.3628-0.36350.46760.47610.27180.1598-0.14270.630.34420.660231.700142.589411.1339
72.5775-0.4685-1.10753.95730.16381.6397-0.33450.2499-0.4603-0.12860.13820.19580.23340.07960.12050.20830.09490.00050.41970.1140.559131.165539.46993.3695
81.6723-0.95680.09816.72660.34551.3161-0.13590.55360.2842-0.45770.08130.3706-0.0239-0.25580.01610.23440.0309-0.02810.59860.03470.220835.501312.8956-2.2155
90.7875-1.09370.47477.75561.01811.87970.30260.1047-0.19310.0576-0.2149-0.0649-0.0797-0.0994-0.03750.1901-0.063-0.01860.53760.04040.327336.827215.39231.2001
101.0370.8056-0.638.18041.77642.99140.01270.5149-0.3168-0.41740.22480.9040.0334-0.7748-0.25190.2883-0.0439-0.1080.4221-0.04280.417628.46047.2682-0.1893
115.8026-0.1722-4.53644.64050.20233.5474-0.13240.57290.1537-0.20370.05010.88340.26250.04750.02660.377-0.0333-0.1520.3422-0.17320.619636.99155.2101-3.1893
121.27910.93391.26277.82345.11193.6816-0.4105-0.36510.79681.7318-0.2044-0.7313-0.31910.09840.12640.4865-0.0594-0.05311.15270.1916-0.196131.338719.013917.7756
132.0204-0.99522.22112.00482.83351.99970.8320.5854-1.24370.5584-0.4467-0.12521.48680.4955-0.53480.52680.0061-0.12270.4192-0.11520.662129.2607-39.175810.9392
147.0174-1.74191.80687.42042.13575.46730.50270.5203-0.81120.0243-0.29730.42760.77970.3607-0.35450.56730.177-0.1150.5026-0.14960.410719.8428-38.89387.4817
155.5676-1.6483-2.27177.6063-0.7821.22690.7659-0.6096-0.64111.7585-0.5187-0.28531.3215-0.2887-0.38571.3985-0.237-0.23750.7517-0.14930.566922.5109-40.668319.0219
161.5266-1.66281.21636.0684-0.32791.2584-0.0959-0.00920.00430.3931-0.15010.57640.19060.51480.27790.25010.02090.10340.4458-0.03880.52821.653-18.88412.9137
172.65510.23791.68662.25771.19952.4402-0.1652-0.94080.211-0.00980.01050.3341-0.17080.17660.14470.307-0.10240.12270.525-0.03880.157533.2519-7.748119.8932
183.29954.4062-0.18742.00911.26780.4609-0.46120.9928-0.3536-1.38850.01831.0667-0.18460.23330.33750.4103-0.0165-0.23990.7597-0.0546-0.087125.6257-12.72780.6517
195.03990.7204-0.55042.5652-0.81443.5786-0.00060.0663-0.21820.1721-0.1221.00440.0797-0.72690.10620.2438-0.08010.04780.5256-0.18120.60197.9575-21.96917.6682
203.254-0.56570.22862.1468-0.27831.75150.0387-0.6331-0.04810.3828-0.0666-0.3670.36290.2442-0.00580.30790.00210.01110.5129-0.14010.727225.5682-24.610710.4748
212.4154-1.29532.00072.3592-0.71563.1896-0.24310.0712-0.53650.1153-0.25090.1017-0.4620.26720.24260.1412-0.095-0.07250.6563-0.19940.240240.9123-12.17470.0199
223.0628-0.75260.16934.4938-1.57463.25590.12790.3127-0.0436-0.8333-0.2381-0.10990.50340.14560.01470.3285-0.09720.09690.386-0.12980.285233.0642-14.4-5.5047
234.56610.14520.02986.2416-2.33023.668-0.4229-0.07990.5544-0.05210.0008-0.14510.1785-0.01880.29330.2103-0.04170.05430.5144-0.08360.450837.8463-13.28461.7261
242.1491-0.1543-0.63753.1394-1.18461.8982-0.09530.08540.175-0.64480.09930.03070.26030.09530.00020.3576-0.07190.25450.5583-0.1230.417345.1146-17.8476-3.2468
256.4137-0.1975-3.5871.78120.65233.0493-0.1562-0.9427-0.05960.6074-0.22830.9305-0.1507-0.4340.05260.627-0.43980.61860.630.0076-0.111830.3178-18.622917.5201
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 93 )
3X-RAY DIFFRACTION3chain 'A' and (resid 94 through 161 )
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 168 )
5X-RAY DIFFRACTION5chain 'A' and (resid 169 through 178 )
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 61 )
7X-RAY DIFFRACTION7chain 'B' and (resid 62 through 87 )
8X-RAY DIFFRACTION8chain 'B' and (resid 88 through 119 )
9X-RAY DIFFRACTION9chain 'B' and (resid 120 through 134 )
10X-RAY DIFFRACTION10chain 'B' and (resid 135 through 154 )
11X-RAY DIFFRACTION11chain 'B' and (resid 155 through 168 )
12X-RAY DIFFRACTION12chain 'B' and (resid 169 through 178 )
13X-RAY DIFFRACTION13chain 'C' and (resid 32 through 44 )
14X-RAY DIFFRACTION14chain 'C' and (resid 45 through 61 )
15X-RAY DIFFRACTION15chain 'C' and (resid 62 through 75 )
16X-RAY DIFFRACTION16chain 'C' and (resid 76 through 93 )
17X-RAY DIFFRACTION17chain 'C' and (resid 94 through 168 )
18X-RAY DIFFRACTION18chain 'C' and (resid 169 through 178 )
19X-RAY DIFFRACTION19chain 'D' and (resid 31 through 75 )
20X-RAY DIFFRACTION20chain 'D' and (resid 76 through 93 )
21X-RAY DIFFRACTION21chain 'D' and (resid 94 through 105 )
22X-RAY DIFFRACTION22chain 'D' and (resid 106 through 128 )
23X-RAY DIFFRACTION23chain 'D' and (resid 129 through 143 )
24X-RAY DIFFRACTION24chain 'D' and (resid 144 through 168 )
25X-RAY DIFFRACTION25chain 'D' and (resid 169 through 178 )

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