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- PDB-8tgb: Crystal structure of root lateral formation protein (RLF) b5-doma... -

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Basic information

Entry
Database: PDB / ID: 8tgb
TitleCrystal structure of root lateral formation protein (RLF) b5-domain from Oryza sativa
Componentsroot lateral formation protein (RLF)
KeywordsOXIDOREDUCTASE / root lateral formation protein / Ncb5or-b5 domain / Cytochrome b5 heme-binding / Oryza sativa / HYDROLASE
Function / homology
Function and homology information


heme binding / metal ion binding / cytosol
Similarity search - Function
Cytochrome b5, heme-binding site / Cytochrome b5 family, heme-binding domain signature. / Cytochrome b5 family, heme-binding domain profile. / Cytochrome b5-like heme/steroid binding domain / Cytochrome b5-like heme/steroid binding domain superfamily / Cytochrome b5-like Heme/Steroid binding domain / Cytochrome b5-like Heme/Steroid binding domain
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Os07g0232200 protein
Similarity search - Component
Biological speciesOryza sativa Japonica Group (Japanese rice)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLovell, S. / Kashipathy, M.M. / Battaile, K.P. / Benson, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110761 United States
CitationJournal: Proteins / Year: 2024
Title: The N-terminal intrinsically disordered region of Ncb5or docks with the cytochrome b 5 core to form a helical motif that is of ancient origin.
Authors: Benson, D.R. / Deng, B. / Kashipathy, M.M. / Lovell, S. / Battaile, K.P. / Cooper, A. / Gao, P. / Fenton, A.W. / Zhu, H.
History
DepositionJul 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: root lateral formation protein (RLF)
B: root lateral formation protein (RLF)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7355
Polymers27,4062
Non-polymers1,3293
Water2,954164
1
A: root lateral formation protein (RLF)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4163
Polymers13,7031
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: root lateral formation protein (RLF)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3202
Polymers13,7031
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.951, 26.138, 82.873
Angle α, β, γ (deg.)90.00, 95.50, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein root lateral formation protein (RLF) / Os07g0232200 protein


Mass: 13703.026 Da / Num. of mol.: 2 / Fragment: Cytochrome b5 heme-binding, K101-E218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice)
Gene: Os07g0232200, OSNPB_070232200 / Plasmid: pET19b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q84YL2
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: JCSG+ A6: 20% (w/v) PEG 1000, 100 mM phosphate-citrate pH 4.2, 200 mM lithium sulfate. Cryoprotectant: 80% crystallization solution and 20% (w/v) glycerol.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Nov 24, 2018
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→45.79 Å / Num. obs: 36463 / % possible obs: 97.6 % / Redundancy: 4.1 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.039 / Rrim(I) all: 0.081 / Χ2: 1.01 / Net I/σ(I): 11 / Num. measured all: 150129
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 98.1 % / Redundancy: 4 % / Rmerge(I) obs: 0.666 / Num. measured all: 7127 / Num. unique obs: 1770 / CC1/2: 0.763 / Rpim(I) all: 0.371 / Rrim(I) all: 0.766 / Χ2: 1.07 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIXdev_3335refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→41.246 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.02 / Phase error: 19.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 1819 4.99 %
Rwork0.175 --
obs0.1762 36453 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→41.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1681 0 91 164 1936
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081836
X-RAY DIFFRACTIONf_angle_d0.9612512
X-RAY DIFFRACTIONf_dihedral_angle_d6.4171236
X-RAY DIFFRACTIONf_chiral_restr0.052252
X-RAY DIFFRACTIONf_plane_restr0.006304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.59190.22281340.2392594X-RAY DIFFRACTION97
1.5919-1.63880.25941430.23042551X-RAY DIFFRACTION94
1.6388-1.69170.23381380.21152649X-RAY DIFFRACTION99
1.6917-1.75220.22621370.20432566X-RAY DIFFRACTION95
1.7522-1.82230.2381350.18762641X-RAY DIFFRACTION99
1.8223-1.90520.1911430.17612623X-RAY DIFFRACTION96
1.9052-2.00570.18631620.16662622X-RAY DIFFRACTION97
2.0057-2.13130.20251270.1622711X-RAY DIFFRACTION100
2.1313-2.29590.20761250.16542658X-RAY DIFFRACTION98
2.2959-2.52690.20011380.16982685X-RAY DIFFRACTION98
2.5269-2.89250.19191480.16812734X-RAY DIFFRACTION99
2.8925-3.64390.2181380.17242741X-RAY DIFFRACTION99
3.6439-41.2460.16841510.16732859X-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)
11.0427-0.09340.65044.54450.95310.6371-0.18590.01440.5557-0.19740.13720.0145-0.8296-0.16290.08860.47560.0151-0.03410.36890.00670.387325.77189.745434.1439
23.2982-0.1612-1.63352.35980.83054.13580.11370.55540.4469-0.1887-0.04020.14560.0448-0.1102-0.04140.16040.01990.01560.24410.04750.21734.75340.505731.5948
32.4107-0.26660.10271.6282-1.33.8938-0.09570.1239-0.0336-0.05920.13330.08250.357-0.0636-0.00310.1489-0.0031-0.02670.2226-0.0110.220248.6454-8.41534.8736
41.24220.07270.8321.9263-0.1591.0267-0.01450.0510.03530.06750.0134-0.1785-0.03060.0803-0.00290.09930.0012-0.02090.12670.00150.166546.4393-7.686647.3588
50.4577-0.5169-0.74541.4890.91551.2336-0.01160.1920.21560.13730.0585-0.02040.0815-0.0242-0.04460.087-0.0033-0.02060.14980.02290.18936.57863.802341.9393
60.88190.45420.11421.4117-0.26860.45960.0238-0.10120.22370.2461-0.00410.0786-0.0613-0.0205-0.02470.11620.0052-0.01280.1286-0.01460.150735.593-1.517552.0088
71.9081-0.0768-0.56391.0444-0.22851.84250.10330.1318-0.0083-0.0780.05140.14740.1991-0.236-0.13390.09920.0105-0.0230.16970.01630.130330.5766-7.606142.0254
82.7321-1.70771.07295.7966-3.31724.43620.00030.1615-0.07140.2503-0.0508-0.3986-0.12540.1294-0.05240.08890.0033-0.03920.1019-0.01160.15144.6739-14.398844.8406
91.87860.5613-1.48680.8145-1.00222.22620.1702-0.2261-0.0820.0033-0.1346-0.2581-0.5840.6752-0.0570.4413-0.1326-0.02970.336-0.00180.231460.96486.89316.6546
101.38120.0296-0.11161.81880.7230.82330.0979-0.22340.1430.12980.01870.1385-0.3636-0.0952-0.04960.27060.01250.04940.19510.02410.154744.15512.57518.4012
110.75840.0861-0.43751.29430.01911.17380.1215-0.01040.08770.00750.02260.106-0.40530.0994-0.11620.2542-0.0020.03710.14610.00950.096250.53217.49127.4585
126.51233.86260.31686.64620.41053.49-0.1299-0.0093-0.2477-0.1175-0.0750.08560.18790.00090.15470.2472-0.01290.01560.1960.02490.167751.0157-3.041716.1007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 111 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 126 )
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 167 )
5X-RAY DIFFRACTION5chain 'A' and (resid 168 through 177 )
6X-RAY DIFFRACTION6chain 'A' and (resid 178 through 197 )
7X-RAY DIFFRACTION7chain 'A' and (resid 198 through 206 )
8X-RAY DIFFRACTION8chain 'A' and (resid 207 through 218 )
9X-RAY DIFFRACTION9chain 'B' and (resid 113 through 139 )
10X-RAY DIFFRACTION10chain 'B' and (resid 140 through 162 )
11X-RAY DIFFRACTION11chain 'B' and (resid 163 through 206 )
12X-RAY DIFFRACTION12chain 'B' and (resid 207 through 216 )

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