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- PDB-6tv2: Heme d1 biosynthesis associated Protein NirF -

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Basic information

Entry
Database: PDB / ID: 6tv2
TitleHeme d1 biosynthesis associated Protein NirF
ComponentsProtein NirF
KeywordsUNKNOWN FUNCTION / 8-bladed beta-propeller / heme d1 biosynthesis / homodimer
Function / homologyCytochrome cd1-nitrite reductase, C-terminal domain superfamily / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / cytoplasm / Protein NirF
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.561 Å
AuthorsKluenemann, T. / Layer, G. / Blankenfeldt, W.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)GRK 2223 Germany
CitationJournal: Febs J. / Year: 2021
Title: Crystal structure of NirF: insights into its role in heme d 1 biosynthesis.
Authors: Klunemann, T. / Nimtz, M. / Jansch, L. / Layer, G. / Blankenfeldt, W.
History
DepositionJan 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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: Protein NirF
B: Protein NirF
C: Protein NirF
D: Protein NirF
E: Protein NirF
F: Protein NirF
G: Protein NirF
H: Protein NirF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,98116
Polymers335,9948
Non-polymers9878
Water64,2963569
1
A: Protein NirF
hetero molecules

H: Protein NirF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2835
Polymers83,9992
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1
2
B: Protein NirF
E: Protein NirF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3004
Polymers83,9992
Non-polymers3012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Protein NirF
G: Protein NirF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1914
Polymers83,9992
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Protein NirF

F: Protein NirF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,2083
Polymers83,9992
Non-polymers2091
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1
Unit cell
Length a, b, c (Å)101.129, 147.830, 108.716
Angle α, β, γ (deg.)90.000, 98.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein NirF


Mass: 41999.281 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: nirF, PA0516 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q51480
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3569 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 10% (w/v) PEG 4000 20% (v/v)glycerol 0.03 NaNO3 0.03 Na2HPO4 0.03 (NH4)2SO4 0.1M MOPS/HEPES pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.561→107.6 Å / Num. obs: 289596 / % possible obs: 94.7 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rpim(I) all: 0.067 / Net I/av σ(I): 6.4 / Net I/σ(I): 6.4
Reflection shellResolution: 1.561→1.73 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 14420 / CC1/2: 0.655 / Rpim(I) all: 0.394 / % possible all: 69.3

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
STARANISOdata scaling
PHENIXdev-3742refinement
PDB_EXTRACT3.25data extraction
DIALSdata reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6rte
Resolution: 1.561→59.46 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.83
RfactorNum. reflection% reflection
Rfree0.2024 14291 4.94 %
Rwork0.1628 --
obs0.1648 289465 64.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.99 Å2 / Biso mean: 22.2603 Å2 / Biso min: 4.05 Å2
Refinement stepCycle: final / Resolution: 1.561→59.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23312 0 104 3569 26985
Biso mean--43.93 31.44 -
Num. residues----2976
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5611-1.57890.2991250.24525654
1.5789-1.59750.3497420.25627746
1.5975-1.61690.263500.242210527
1.6169-1.63740.2642800.2619138810
1.6374-1.6590.2883850.2459176012
1.659-1.68170.25931000.2454208015
1.6817-1.70570.28731580.2526260219
1.7057-1.73120.29581860.2578361926
1.7312-1.75820.28122420.2376465133
1.7582-1.78710.27552800.2382569740
1.7871-1.81790.26753580.2326669448
1.8179-1.85090.26763980.228786656
1.8509-1.88650.2344600.2203909464
1.8865-1.9250.24025350.2144997371
1.925-1.96690.26115650.20331073376
1.9669-2.01270.24446040.18871149081
2.0127-2.0630.2436110.1911227887
2.063-2.11880.22137120.18241314093
2.1188-2.18110.22876960.16951386998
2.1811-2.25150.22866660.168514135100
2.2515-2.3320.20447220.16514164100
2.332-2.42540.21867660.164814070100
2.4254-2.53580.20977420.159214166100
2.5358-2.66940.20917680.160614101100
2.6694-2.83670.21197450.151914144100
2.8367-3.05570.19637510.152314176100
3.0557-3.36320.17497670.148514135100
3.3632-3.84980.15857200.129414199100
3.8498-4.850.1497160.113114247100
4.85-59.460.18387410.173714312100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.93920.0267-0.11030.9483-0.05911.43420.00330.12430.1017-0.17210.03030.2494-0.1033-0.1037-0.01880.08040.0035-0.0490.07510.03390.121342.3989-65.545-18.8777
20.72810.1990.41271.89140.54460.87630.0115-0.07620.19930.04020.02050.1034-0.1321-0.0412-0.02630.06670.00510.03320.0626-0.01570.133945.7739-51.3496-1.3023
32.70950.2162-1.88790.65980.19181.77750.0644-0.1310.12160.0572-0.0207-0.055-0.0890.187-0.01830.0742-0.0116-0.0420.0847-0.01360.118764.8603-57.0833-3.9185
41.35530.11430.35160.60130.27580.4448-0.04670.12680.0265-0.12810.0234-0.0213-0.0530.04850.01820.0936-0.0134-0.0080.07420.00910.043463.4048-69.8246-20.7277
50.9174-0.03460.17441.0444-0.14771.51750.02990.0822-0.055-0.1503-0.0126-0.14970.1390.1113-0.01730.08760.00710.02520.0696-0.0150.056566.3836-46.5491-72.5083
61.18050.7889-0.42031.8091-1.18340.9326-0.0255-0.0729-0.262-0.12180.0093-0.21740.19460.02830.02340.1132-0.0035-0.01620.07530.02160.098366.0952-61.1691-58.5339
71.42850.1779-0.32221.9403-0.0951.40790.0537-0.2517-0.15360.14760.03360.14640.1063-0.0582-0.05380.1035-0.030.00260.10420.05280.114154.6471-56.7497-51.008
83.18410.01491.32782.1233-1.30862.80590.1071-0.1308-0.1350.05710.00810.21920.0593-0.0702-0.08780.0746-0.02620.04120.11840.02170.171540.7435-54.9448-60.4003
91.59120.0513-0.5321.0221-0.25810.7563-0.02940.1425-0.037-0.11880.03190.1510.0529-0.0975-0.01110.087-0.0165-0.01370.0863-0.00280.062645.3643-42.5394-74.2706
101.1536-0.2313-0.25960.60790.2191.08980.2081-0.27110.3890.27190.0038-0.5002-0.0660.14340.14420.1775-0.0342-0.19730.06710.08070.159315.8142-30.8899-35.6387
110.7318-0.04740.06151.8478-0.49620.77920.0850.14860.24960.0228-0.111-0.3739-0.16730.09680.01980.1317-0.01130.01510.09410.08230.238213.5601-18.4216-53.6259
122.8233-1.0342-1.36992.61490.89963.03840.10260.10110.2229-0.0842-0.1103-0.0227-0.1824-0.21810.02180.08640.0115-0.030.10830.01790.107-4.5091-21.8459-52.4231
131.1431-0.05440.07551.0484-0.40360.5625-0.0194-0.0759-0.00250.3204-0.07550.0069-0.1022-0.04650.07390.2158-0.0238-0.03430.1041-0.03020.0399-6.415-34.4232-35.7128
140.7888-0.41670.13410.95040.01480.9869-0.02630.2730.0061-0.3160.0108-0.1259-0.15370.23830.0540.127-0.03960.07860.1941-0.01420.0387.054-2.9385-21.4383
151.11570.37270.01211.5861-0.26081.01080.01920.0028-0.10510.01150.0101-0.00930.1157-0.0517-0.00250.0547-0.00460.0120.0733-0.01680.0458-0.5309-16.0392-3.8768
162.97120.2798-0.40721.5454-1.33252.4303-0.1774-0.1466-0.1846-0.36010.1021-0.03110.56590.0552-0.00190.1524-0.0030.03420.1315-0.04590.1034-21.0798-8.5221-10.0667
170.996-0.0489-0.52180.8934-0.03911.3224-0.0020.247-0.0106-0.2115-0.0470.10070.0131-0.10920.02130.1404-0.0011-0.01680.1184-0.02050.0428-11.30760.1388-21.8433
181.3392-0.12750.75811.3538-0.52970.6949-0.0180.03210.1198-0.0142-0.023-0.1467-0.02580.07410.01740.0596-0.01970.03850.0664-0.01930.085769.4767-20.5579-61.87
192.6560.4598-0.06980.4699-0.25890.4450.00770.06840.266-0.16780.0155-0.1595-0.20860.0109-0.05110.1248-0.00290.03140.06580.01950.104958.6023-13.6409-67.0215
201.4567-0.3712-0.30721.66610.21481.6081-0.0419-0.09250.09190.0372-0.03570.2464-0.0553-0.16880.05070.06840.01160.00420.1019-0.02230.112243.4041-13.6053-60.8469
214.33410.71940.12682.7707-1.73833.074-0.1204-0.15050.07370.19510.09870.1827-0.0903-0.20370.05130.15450.02320.06290.1935-0.03820.122646.7266-20.5458-42.2132
221.8703-0.1445-0.42590.73570.13790.7747-0.0201-0.30850.09760.28430.03060.07330.0202-0.0826-0.0170.15630.00310.02090.1584-0.01950.074461.2199-28.3719-41.886
231.64240.35510.23861.1832-0.12230.4842-0.0096-0.06080.02410.09640.0143-0.0521-0.0012-0.002-0.01270.07390.00340.02940.0734-0.02480.034366.5349-28.6063-52.7401
241.23080.17040.43921.1751-0.03630.7631-0.0438-0.10660.20130.1363-0.02750.1571-0.1264-0.05150.0480.06830.02010.00320.0704-0.03210.0987-8.4109-51.56858.7351
251.24390.2819-0.15361.5583-0.03620.7381-0.0635-0.00160.23580.0902-0.0405-0.1057-0.050.10080.05820.063-0.0328-0.06880.09210.02770.133514.7848-46.67476.3587
262.04230.0971-0.39192.12390.86461.9766-0.26060.32330.2972-0.0883-0.026-0.1794-0.14410.2770.21390.1371-0.0367-0.05890.16380.08260.137911.727-54.2671-12.0415
271.42730.2727-0.25670.956-0.15450.6724-0.05940.1830.0539-0.1782-0.01030.00570.00050.07320.05310.0974-0.0113-0.02040.09810.01830.0592-2.926-61.9042-12.2722
281.719-0.77440.20271.4432-0.02350.6542-0.0540.00760.1358-0.043-0.02380.0964-0.00650.02380.07280.0282-0.00820.00440.06690.020.0658-8.5606-61.6613-1.8264
291.4614-0.2691-0.66691.1655-0.22940.9496-0.0149-0.0422-0.10890.1283-0.0945-0.31770.10040.12560.08330.0866-0.0041-0.03730.08890.0550.200318.9422-57.4986-45.8781
301.7038-0.47750.36920.75680.20640.4127-0.0282-0.1251-0.10640.3442-0.0834-0.21750.11230.0650.05870.1813-0.0164-0.03840.09320.06290.157812.0586-62.1956-39.6839
311.42260.24570.48991.98240.19061.6058-0.01460.0096-0.19210.0609-0.04020.16290.1584-0.12170.04190.0986-0.0310.03710.0767-0.02480.1286-6.411-64.6741-45.9495
325.3664-0.17190.25196.071.59215.19780.04630.2322-0.0881-0.429-0.17850.0770.31210.02820.08120.16720.00630.02520.1532-0.02220.1087-3.0401-61.7467-63.8806
336.64690.695-1.43681.9684-1.2784.04860.04180.33170.1159-0.01140.03880.1273-0.1108-0.2317-0.04020.13720.0251-0.04220.1507-0.02370.1253-5.334-52.6292-66.4992
342.2194-0.21010.35861.4231-0.06850.65250.11410.3164-0.0833-0.2497-0.1359-0.11050.03180.02210.0180.13030.02080.04110.15290.0190.119710.6952-50.2679-65.6418
351.3885-0.6491-0.02271.4348-0.13890.7330.0550.16350.0139-0.1154-0.1172-0.2462-0.05810.00440.0580.0738-0.0087-0.00040.09610.02450.140916.0782-49.6713-54.9546
361.40860.2902-0.33711.1724-0.11560.5111-0.043-0.0901-0.14460.03750.0218-0.21580.05840.08890.020.05260.0172-0.02120.0643-0.00240.107559.1598-18.91218.8471
371.32460.11770.57771.42760.07581.1545-0.03320.0074-0.1330.02010.01630.14020.0395-0.07010.0160.0349-0.01060.02080.0627-0.0090.084135.9519-24.11856.4526
383.2979-0.3750.29223.528-1.1453.1164-0.1390.1885-0.2148-0.05150.11150.10780.1544-0.19360.03420.0922-0.03040.00460.1308-0.0390.101538.9115-16.5953-12.1569
392.03510.37570.47091.10030.29960.8543-0.03940.2753-0.124-0.22690.0563-0.0372-0.00660.007-0.0170.1118-0.01980.01510.1116-0.01140.064653.4969-9.022-12.1877
401.2712-0.3785-0.32661.0187-0.24910.8635-0.02790.0708-0.0718-0.04-0.0224-0.1033-0.01710.00310.04620.0532-0.0195-0.02120.0591-0.02960.075959.1739-8.7958-1.9218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 105 )A7 - 105
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 182 )A106 - 182
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 267 )A183 - 267
4X-RAY DIFFRACTION4chain 'A' and (resid 268 through 378 )A268 - 378
5X-RAY DIFFRACTION5chain 'B' and (resid 7 through 105 )B7 - 105
6X-RAY DIFFRACTION6chain 'B' and (resid 106 through 148 )B106 - 148
7X-RAY DIFFRACTION7chain 'B' and (resid 149 through 215 )B149 - 215
8X-RAY DIFFRACTION8chain 'B' and (resid 216 through 267 )B216 - 267
9X-RAY DIFFRACTION9chain 'B' and (resid 268 through 378 )B268 - 378
10X-RAY DIFFRACTION10chain 'C' and (resid 7 through 105 )C7 - 105
11X-RAY DIFFRACTION11chain 'C' and (resid 106 through 177 )C106 - 177
12X-RAY DIFFRACTION12chain 'C' and (resid 178 through 247 )C178 - 247
13X-RAY DIFFRACTION13chain 'C' and (resid 248 through 378 )C248 - 378
14X-RAY DIFFRACTION14chain 'D' and (resid 7 through 73 )D7 - 73
15X-RAY DIFFRACTION15chain 'D' and (resid 74 through 247 )D74 - 247
16X-RAY DIFFRACTION16chain 'D' and (resid 248 through 284 )D248 - 284
17X-RAY DIFFRACTION17chain 'D' and (resid 285 through 378 )D285 - 378
18X-RAY DIFFRACTION18chain 'E' and (resid 7 through 77 )E7 - 77
19X-RAY DIFFRACTION19chain 'E' and (resid 78 through 105 )E78 - 105
20X-RAY DIFFRACTION20chain 'E' and (resid 106 through 220 )E106 - 220
21X-RAY DIFFRACTION21chain 'E' and (resid 221 through 267 )E221 - 267
22X-RAY DIFFRACTION22chain 'E' and (resid 268 through 349 )E268 - 349
23X-RAY DIFFRACTION23chain 'E' and (resid 350 through 378 )E350 - 378
24X-RAY DIFFRACTION24chain 'F' and (resid 7 through 105 )F7 - 105
25X-RAY DIFFRACTION25chain 'F' and (resid 106 through 220 )F106 - 220
26X-RAY DIFFRACTION26chain 'F' and (resid 221 through 267 )F221 - 267
27X-RAY DIFFRACTION27chain 'F' and (resid 268 through 349 )F268 - 349
28X-RAY DIFFRACTION28chain 'F' and (resid 350 through 378 )F350 - 378
29X-RAY DIFFRACTION29chain 'G' and (resid 7 through 73 )G7 - 73
30X-RAY DIFFRACTION30chain 'G' and (resid 74 through 99 )G74 - 99
31X-RAY DIFFRACTION31chain 'G' and (resid 100 through 220 )G100 - 220
32X-RAY DIFFRACTION32chain 'G' and (resid 221 through 247 )G221 - 247
33X-RAY DIFFRACTION33chain 'G' and (resid 248 through 267 )G248 - 267
34X-RAY DIFFRACTION34chain 'G' and (resid 268 through 349 )G268 - 349
35X-RAY DIFFRACTION35chain 'G' and (resid 350 through 378 )G350 - 378
36X-RAY DIFFRACTION36chain 'H' and (resid 7 through 105 )H7 - 105
37X-RAY DIFFRACTION37chain 'H' and (resid 106 through 220 )H106 - 220
38X-RAY DIFFRACTION38chain 'H' and (resid 221 through 267 )H221 - 267
39X-RAY DIFFRACTION39chain 'H' and (resid 268 through 349 )H268 - 349
40X-RAY DIFFRACTION40chain 'H' and (resid 350 through 378 )H350 - 378

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