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- PDB-6jc0: Structural analysis of molybdopterin synthases from two mycobacte... -

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Basic information

Entry
Database: PDB / ID: 6jc0
TitleStructural analysis of molybdopterin synthases from two mycobacteria pathogens
Components
  • Putative molybdenum cofactor biosynthesis protein
  • Putative molybdenum cofactor biosynthesis protein D2 (MoaD2) / thiamine S
KeywordsTRANSFERASE / molybdopterin synthases / molybdenum cofactor biosynthesis / sulfur transfer
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process
Similarity search - Function
Molybdopterin biosynthesis MoaE subunit / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Aldehyde Oxidoreductase; domain 3 / Beta-grasp domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Putative molybdenum cofactor biosynthesis protein / Putative molybdenum cofactor biosynthesis protein D2 (MoaD2) / thiamine S
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, X. / Wang, H.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of ChinaGrant Nos. 813300237 and 81520108019 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Structural analysis of molybdopterin synthases from two mycobacterial pathogens.
Authors: Wang, H. / Chen, X. / Zhang, W. / Zhou, W. / Liu, X. / Rao, Z.
History
DepositionJan 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
B: Putative molybdenum cofactor biosynthesis protein
C: Putative molybdenum cofactor biosynthesis protein D2 (MoaD2) / thiamine S
D: Putative molybdenum cofactor biosynthesis protein
A: Putative molybdenum cofactor biosynthesis protein D2 (MoaD2) / thiamine S


Theoretical massNumber of molelcules
Total (without water)49,1944
Polymers49,1944
Non-polymers00
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-30 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.763, 57.599, 66.577
Angle α, β, γ (deg.)90.00, 99.29, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative molybdenum cofactor biosynthesis protein


Mass: 15308.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: moaE2, MSMEI_5550 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7FL16
#2: Protein Putative molybdenum cofactor biosynthesis protein D2 (MoaD2) / thiamine S


Mass: 9288.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: moaD2, MSMEI_5548 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I7FT00
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: Ammonium citrate dibasic, Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 27904 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.61 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.041 / Rrim(I) all: 0.101 / Rsym value: 0.094 / Χ2: 0.971 / Net I/σ(I): 16.8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1342 / CC1/2: 0.964 / Rpim(I) all: 0.165 / Rrim(I) all: 0.427 / Rsym value: 0.313 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JBZ

6jbz


Resolution: 2.1→49.208 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.54
RfactorNum. reflection% reflection
Rfree0.2368 1362 5.04 %
Rwork0.19 --
obs0.1925 27039 95.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→49.208 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 0 225 3579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043405
X-RAY DIFFRACTIONf_angle_d0.7354634
X-RAY DIFFRACTIONf_dihedral_angle_d13.0711220
X-RAY DIFFRACTIONf_chiral_restr0.027556
X-RAY DIFFRACTIONf_plane_restr0.003606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15640.29241030.21191903X-RAY DIFFRACTION72
2.1564-2.24280.28071200.21352399X-RAY DIFFRACTION90
2.2428-2.34480.28781410.19982583X-RAY DIFFRACTION97
2.3448-2.46850.27351420.21152649X-RAY DIFFRACTION99
2.4685-2.62310.28991380.21512671X-RAY DIFFRACTION99
2.6231-2.82560.24541480.20692659X-RAY DIFFRACTION100
2.8256-3.10990.25421410.20422669X-RAY DIFFRACTION100
3.1099-3.55980.23511230.18762717X-RAY DIFFRACTION100
3.5598-4.48460.20191390.16812711X-RAY DIFFRACTION100
4.4846-49.2080.19611670.1692716X-RAY DIFFRACTION99
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)
10.03580.02470.0380.0176-0.04160.30870.030.03780.4384-0.0969-0.0582-0.00480.0396-0.2490.01310.15230.0260.0460.1385-0.0020.289718.735521.051-10.6315
20.01290.00430.00250.0020.002-0.00070.0616-0.04950.1801-0.0380.196-0.1428-0.12580.1227-0.00020.28480.01510.11490.1663-0.03720.408614.098122.8819-3.199
30.0349-0.016-0.00110.0126-0.01190.04-0.0143-0.05790.033-0.07250.0301-0.0776-0.0313-0.08730.03760.1508-0.03840.03090.2324-0.08580.142717.721917.46492.1424
40.009-0.00850.00670.0064-0.00120.00710.1176-0.16050.0020.094-0.01170.03760.03740.094600.1769-0.0424-0.00390.23110.00210.142740.80922.12594.4157
50.3484-0.1612-0.20770.20630.18480.19540.27180.08010.3034-0.2288-0.1062-0.1239-0.1096-0.00240.10170.1607-0.00730.00480.1029-0.00320.137236.157522.3615-10.2513
60.01710.01570.00540.0045-0.001-0.0020.10240.0734-0.1221-0.0666-0.12660.22330.1668-0.07650.00010.14640.0109-0.0280.1801-0.04190.162120.33529.3629-13.4837
70.00860.00310.01780.0073-0.00280.02220.189-0.0062-0.0771-0.0233-0.12050.1831-0.1001-0.12590.00210.1119-0.02160.01070.1822-0.04080.244614.232812.2946-5.5491
80.106-0.085-0.0710.1107-0.09750.5359-0.0158-0.05330.1932-0.0741-0.02790.0020.0341-0.31930.00350.1096-0.03880.03760.1165-0.02710.163823.658921.3356-3.0617
90.0934-0.08960.09890.5182-0.63120.7633-0.1043-0.0470.00860.1138-0.2545-0.03720.2296-0.1054-0.30860.1157-0.06880.04610.1393-0.08270.149720.98138.4486-0.9575
100.0136-0.0142-0.01010.04140.0320.05670.1636-0.1364-0.14020.0198-0.0666-0.2457-0.04030.1498-0.00070.1616-0.0353-0.00290.1477-0.00310.14642.16719.9729-6.8582
110.11460.0488-0.03050.1554-0.15540.26680.1224-0.01120.04450.1352-0.05490.166-0.2662-0.10450.00760.1421-0.00050.00860.1702-0.02850.1632-8.301815.597639.2437
120.1625-0.0722-0.09020.05710.02280.06460.06180.2728-0.1381-0.1273-0.0575-0.13650.2197-0.38590.00250.1883-0.07070.01250.2262-0.01890.1517-11.16836.856333.4987
130.1019-0.13430.00230.36220.13490.44780.232-0.0218-0.2349-0.1642-0.0114-0.1523-0.05930.35670.09570.1083-0.0376-0.01760.19940.00790.15871.238410.948236.5129
140.02810.05610.02280.11260.05260.0251-0.01280.02370.11790.0805-0.00080.1477-0.17290.00230.00550.11310.0028-0.02230.11040.0160.098721.361124.21719.631
150.00770.0032-0.0008-0.0038-0.0039-0.00250.0060.0254-0.0198-0.33090.1340.0652-0.1821-0.0840.00010.2809-0.0017-0.00430.16620.01040.284713.495527.719511.2994
160.1846-0.106-0.03240.18430.1780.2358-0.0128-0.05870.20130.00230.2119-0.0504-0.07550.24110.01430.174-0.05590.03460.2418-0.02730.163221.8921.42417.8018
170.32680.1740.12670.6880.02810.05580.10490.25580.10340.10830.04550.37930.0434-0.06880.2726-0.0158-0.0374-0.21080.4352-0.06440.0628-3.116716.91312.1688
180.38040.33860.41531.08880.68090.5784-0.06-0.1420.03770.3777-0.1253-0.05640.1177-0.0241-0.18320.1694-0.0172-0.03040.14220.05480.093117.051618.218925.0128
190.560.28370.27361.06970.5590.7861-0.110.2035-0.0742-0.34540.4638-0.4355-0.21360.17680.6040.09770.0121-0.0250.06820.1537-0.015615.393519.992712.8262
200.60570.24750.50740.58170.3521.2720.00050.115-0.25980.15320.1302-0.07620.10720.15770.26510.10370.00710.00650.0721-0.00830.122518.573111.210213.7293
210.0714-0.05610.05340.0628-0.06420.06550.11790.1334-0.2161-0.01780.03710.07380.2748-0.10220.00220.15780.0029-0.02260.25220.01230.1394-6.126814.383216.1499
220.2133-0.2684-0.11850.35830.18270.13220.07770.31520.0935-0.5079-0.0381-0.14620.05740.03520.00970.3766-0.05490.1079-0.11830.15390.088144.323113.3499-27.0401
230.1305-0.034-0.0690.0957-0.03920.0689-0.14830.0972-0.0637-0.0899-0.0447-0.1230.02350.0722-0.16540.7421-0.05870.33750.15440.11060.266147.100614.2382-30.0174
240.3505-0.19660.39330.1161-0.22750.44830.28520.1354-0.0273-0.30640.3192-0.13360.20330.21120.04180.2175-0.02070.02670.2155-0.03430.201748.48293.0518-27.9242
250.02410.0012-0.00510.0072-0.01540.088-0.0204-0.00040.11090.09260.082-0.1693-0.2510.2571-0.00030.1323-0.01350.02610.1261-0.01660.157752.103210.5421-16.9392
260.61860.1467-0.23350.38640.09560.50730.29150.07360.1223-0.3354-0.16220.233-0.2483-0.17040.33080.14030.089-0.09980.06150.02040.046638.01176.1159-23.567
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 2 through 16 )
2X-RAY DIFFRACTION2chain 'B' and (resid 17 through 25 )
3X-RAY DIFFRACTION3chain 'B' and (resid 29 through 38 )
4X-RAY DIFFRACTION4chain 'B' and (resid 39 through 47 )
5X-RAY DIFFRACTION5chain 'B' and (resid 48 through 58 )
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 73 )
7X-RAY DIFFRACTION7chain 'B' and (resid 74 through 84 )
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 104 )
9X-RAY DIFFRACTION9chain 'B' and (resid 105 through 122 )
10X-RAY DIFFRACTION10chain 'B' and (resid 123 through 141 )
11X-RAY DIFFRACTION11chain 'C' and (resid 5 through 35 )
12X-RAY DIFFRACTION12chain 'C' and (resid 36 through 56 )
13X-RAY DIFFRACTION13chain 'C' and (resid 57 through 88 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 10 )
15X-RAY DIFFRACTION15chain 'D' and (resid 11 through 24 )
16X-RAY DIFFRACTION16chain 'D' and (resid 25 through 38 )
17X-RAY DIFFRACTION17chain 'D' and (resid 39 through 58 )
18X-RAY DIFFRACTION18chain 'D' and (resid 59 through 72 )
19X-RAY DIFFRACTION19chain 'D' and (resid 73 through 104 )
20X-RAY DIFFRACTION20chain 'D' and (resid 105 through 122 )
21X-RAY DIFFRACTION21chain 'D' and (resid 123 through 141 )
22X-RAY DIFFRACTION22chain 'A' and (resid 5 through 21 )
23X-RAY DIFFRACTION23chain 'A' and (resid 22 through 31 )
24X-RAY DIFFRACTION24chain 'A' and (resid 32 through 43 )
25X-RAY DIFFRACTION25chain 'A' and (resid 44 through 56 )
26X-RAY DIFFRACTION26chain 'A' and (resid 57 through 88 )

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