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- PDB-6xri: MSMEG_2027 domain-swapped dimer -

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Basic information

Entry
Database: PDB / ID: 6xri
TitleMSMEG_2027 domain-swapped dimer
ComponentsUncharacterized protein
KeywordsOXIDOREDUCTASE / F420 / Quinone / Reductase
Function / homologyF420H(2)-dependent quinone reductase / F420H(2)-dependent quinone reductase / coenzyme F420 binding / FMN-binding split barrel / oxidoreductase activity / plasma membrane / Nitroreductase
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsJackson, C.J. / Antoney, J.P. / Ahmed, F.H.
CitationJournal: To Be Published
Title: Structure of F420-H2 dependent oxidoreductase MSMEG_2027 in dimeric apo form.
Authors: Jackson, C.J. / Antoney, J.P.
History
DepositionJul 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
I: Uncharacterized protein
J: Uncharacterized protein
K: Uncharacterized protein
L: Uncharacterized protein
M: Uncharacterized protein
N: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)224,39214
Polymers224,39214
Non-polymers00
Water9,890549
1
A: Uncharacterized protein
F: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,0562
Polymers32,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-24 kcal/mol
Surface area13590 Å2
MethodPISA
2
B: Uncharacterized protein
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,0562
Polymers32,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-22 kcal/mol
Surface area13550 Å2
MethodPISA
3
D: Uncharacterized protein
E: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,0562
Polymers32,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-24 kcal/mol
Surface area13380 Å2
MethodPISA
4
G: Uncharacterized protein
H: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,0562
Polymers32,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-24 kcal/mol
Surface area13460 Å2
MethodPISA
5
I: Uncharacterized protein
J: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,0562
Polymers32,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-22 kcal/mol
Surface area13220 Å2
MethodPISA
6
K: Uncharacterized protein
L: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,0562
Polymers32,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-23 kcal/mol
Surface area13160 Å2
MethodPISA
7
M: Uncharacterized protein
N: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,0562
Polymers32,0562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-24 kcal/mol
Surface area13160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.554, 110.228, 140.150
Angle α, β, γ (deg.)90.000, 105.213, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Uncharacterized protein


Mass: 16028.034 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_2027 / Plasmid: pETMCSIII / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0QU01
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.55 Å3/Da / Density % sol: 51.73 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 13% PEG 8000, 0.1 M Tris, 20% Isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 17, 2013
RadiationMonochromator: Silicon Double Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.37→34.21 Å / Num. obs: 81362 / % possible obs: 92.9 % / Redundancy: 3.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.205 / Rpim(I) all: 0.123 / Rrim(I) all: 0.239 / Χ2: 0.51 / Net I/av σ(I): 3.9 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.37-2.423.81.7031780746700.521.0071.9810.698.3
12.31-34.213.40.03120586070.9990.020.03712.592.5

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Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XDS20200417data reduction
Aimless0.7.4data scaling
PHASER5.8.0073phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4y9i

4y9i


Resolution: 2.37→34.18 Å / Cross valid method: FREE R-VALUE / σ(F): 1.08 / Phase error: 33.5716
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.3009 4039 4.97 %0
Rwork0.2416 77215 --
obs0.2494 81254 92.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.2 Å2
Refinement stepCycle: LAST / Resolution: 2.37→34.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15180 0 0 549 15729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008715609
X-RAY DIFFRACTIONf_angle_d0.86121236
X-RAY DIFFRACTIONf_chiral_restr0.04972276
X-RAY DIFFRACTIONf_plane_restr0.00632749
X-RAY DIFFRACTIONf_dihedral_angle_d22.30555879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.410.33472420.2833991X-RAY DIFFRACTION92.49
2.41-2.450.29252140.28134118X-RAY DIFFRACTION93.85
2.45-2.50.32632390.27173983X-RAY DIFFRACTION93.21
2.5-2.550.28332250.26924143X-RAY DIFFRACTION93.75
2.55-2.610.3092150.2664062X-RAY DIFFRACTION93.64
2.61-2.650.2871380.26492840X-RAY DIFFRACTION65.39
2.68-2.740.26921850.24843260X-RAY DIFFRACTION74.5
2.74-2.810.31132490.25974082X-RAY DIFFRACTION93.2
2.81-2.890.311930.25094102X-RAY DIFFRACTION94.32
2.89-2.990.29262210.24734096X-RAY DIFFRACTION93.77
2.99-3.090.29042280.25144121X-RAY DIFFRACTION93.96
3.09-3.220.26731890.23894126X-RAY DIFFRACTION94.79
3.22-3.360.32371990.24474151X-RAY DIFFRACTION94.34
3.36-3.540.3842050.29684018X-RAY DIFFRACTION92.22
3.54-3.760.36441180.26192300X-RAY DIFFRACTION52.37
3.76-4.050.40951670.2683108X-RAY DIFFRACTION70.77
4.05-4.460.23142050.19874146X-RAY DIFFRACTION94.46
4.46-5.10.26931810.19074197X-RAY DIFFRACTION95.06
5.1-6.420.26572170.22594161X-RAY DIFFRACTION94.31
6.42-34.180.32321960.25054223X-RAY DIFFRACTION93.7
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)
10.376766687776-0.01421440953380.1478158346550.220578332353-0.2852921449470.454050372675-0.0691244071808-0.2086698046250.1004324262820.269289095421-0.05888499973950.0853957386773-0.329963935236-0.111766951062-0.2449100225460.125970122857-0.02157463116870.07299721571530.109761143233-0.0681952962127-0.0220196093336-24.63194398234.54095509608-55.4738656306
20.369316725575-0.0645678767528-0.1158440742220.319847364510.4567214785180.659677057053-0.0002865965082590.04932375860810.0795430598051-0.237619891866-0.1610535731040.180730283214-0.136478844736-0.2654062663690.119241377510.9864470926260.0162548913045-0.1018436238330.338223650011-0.04568855975340.239746834778-60.92412981594.447595401382.97410361643
30.190520038186-0.00526981166760.124613498790.0914922202529-0.1068006048020.206601764133-0.07898839614070.0298968446205-0.0268452158815-0.198367708591-0.0196421259797-0.04259430140270.08770229180280.0666549166620.07673227993710.9998459593530.02736337562020.005822758658310.2070718166910.04667132220570.217105085052-49.4715642236-4.531212355951.36075215492
40.0881686883418-0.102428448892-0.04008044907570.2916460871480.3250738024260.4579099389980.00679218667763-0.0396189648713-0.002386226223540.113628201286-0.03943142128890.0797273134225-0.017461492057-0.1347662307580.06929550721341.39424129293-0.1959625970650.3024841357120.431548920991-0.07490063267970.388646505317-25.40971163534.5209388482721.0991216081
50.278080774287-0.2104889991780.203285558810.208537673582-0.2217842836270.259644288829-0.00791123234165-0.151031714283-0.06057098109920.178832725370.04513145107790.006207629644550.05963544310970.09442221085160.03234351514741.43945924545-0.164309845513-0.08877925305540.4436097423260.08746284453930.321428471166-13.8305151752-4.4711769619.3963154834
60.142803270286-0.04938611671430.07309681096240.0166182652342-0.006255035438070.104718528690.0226284341331-0.0936852892708-0.08123311477790.1319183843050.0528532568078-0.03374611720090.1199968472930.02685245969160.1575718476180.290688552922-0.00937068650232-0.1401209937990.03673237788980.0395056400639-0.160264828618-13.303314373-4.51246693568-57.3419824914
70.0749909931088-0.04143518354870.001479436790310.0500187391598-0.08097162755360.2078731127320.01137094457440.07208388340440.112715594374-0.241689528971-0.00680634286123-0.0657411100175-0.2378810266010.1580971454510.05120875108370.497563406074-0.1375620772580.03789783252260.1259528277040.0279337814341-0.102428666637-48.9691613234-4.2726417431541.4697856083
80.1391964364720.01285886151570.03009260593950.201463057312-0.1969139010780.686585297734-0.0374276968616-0.02206003295710.02433654232820.06993870282030.0322813160088-0.00569115080398-0.0905027707232-0.0616340601376-0.02596093980320.74434601728-0.0927953593959-0.03718326649910.1602653014010.02959724395440.042736319038-60.33632252994.7360668938439.5977753274
90.04879947636310.0151970813907-0.06351901245640.129115947791-0.1849044938520.3118150755560.0168975707294-0.04116460447070.02711451275270.101061232798-0.0703897577274-0.0383238716264-0.01605937952450.131862916985-0.01284453662560.796076276510.00649524658101-0.03630387745040.1174477914610.099366485832-0.094457546893-12.0942501728-3.94557280768-17.2646288509
100.1683955944070.083819869120.1110611943520.1400073332440.1339187555190.39285765657-0.0537769659394-0.08531064674980.05570568207820.130183574288-0.05017954046060.074658935444-0.0675081259695-0.08853169949890.02427575560190.8026623141370.02076294290840.01450680152270.13862429067-0.04769003779030.0679991315946-23.34577608854.72986663477-19.003005335
110.245755871243-0.4075658548710.2260533888420.692534497338-0.3875383365920.2175183234890.003320930921870.1281901698010.139783225025-0.322727235707-0.145158178438-0.407207344009-0.02486569076740.1577037671670.1305560949191.07754782554-0.08545689340470.03994315792490.4153966144270.03753459013160.38325288005-49.7784293932-4.39428901794-35.5650521143
120.502268893391-0.178585198969-0.2284090482641.373842666140.1839129128740.856695319491-0.1159312999970.0925287059469-0.0339243157211-0.238378700351-0.06291460303370.0297243853876-0.0578446987479-0.04928989724740.09540994035451.22597924292-0.045149268031-0.2518265642090.343464727645-0.04801541468830.494630577715-61.82912665675.84432522846-36.3367009501
130.80570253656-0.5685434736520.2195087965931.08795036616-0.2218543658790.8962630232090.051595206952-0.02117615023030.0108522756944-0.212837978206-0.1601714273770.02647703804220.129336695518-0.08484452982960.01004663125330.566494717823-0.0645392547489-0.1561417980.197829867280.0639958757370.326048298073-10.0065786956-4.5715580744359.2570754831
141.093652626420.0290768485731-0.2034018669690.267773766479-0.1354846284111.19388652716-0.0468030468478-0.2168073704110.3436509903630.187316305232-0.1470952162980.108546471263-0.334540384056-0.1075710421780.1395038391471.058152848230.0245528897075-0.1418310925350.344854145314-0.04671729907240.507459565526-21.65446818564.7676426374758.4357361284
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 6 through 140)AA6 - 1401 - 135
22(chain 'B' and resid 6 through 140)BB6 - 1401 - 135
33(chain 'C' and resid 7 through 140)CC7 - 1401 - 135
44(chain 'D' and resid 6 through 140)DD6 - 1401 - 135
55(chain 'E' and resid 7 through 140)EE7 - 1401 - 134
66(chain 'F' and resid 7 through 140)FF7 - 1401 - 134
77(chain 'G' and resid 6 through 140)GG6 - 1401 - 135
88(chain 'H' and resid 7 through 140)HH7 - 1401 - 134
99(chain 'I' and resid 6 through 140)II6 - 1401 - 136
1010(chain 'J' and resid 7 through 140)JJ7 - 1401 - 134
1111(chain 'K' and resid 6 through 140)KK6 - 1401 - 135
1212(chain 'L' and resid 12 through 140)LL12 - 1401 - 129
1313(chain 'M' and resid 6 through 140)MM6 - 1401 - 135
1414(chain 'N' and resid 9 through 140)NN9 - 1401 - 132

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