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- PDB-7xrz: Crystal structure of BRIL and SRP2070_Fab complex -

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Basic information

Entry
Database: PDB / ID: 7xrz
TitleCrystal structure of BRIL and SRP2070_Fab complex
Components
  • IGG HEAVY CHAIN
  • IGG LIGHT CHAIN
  • Soluble cytochrome b562
KeywordsIMMUNE SYSTEM / BRIL / antibody / complex
Function / homology
Function and homology information


electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Soluble cytochrome b562
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSuzuki, M. / Miyagi, H. / Yasunaga, M. / Asada, H. / Iwata, S. / Saito, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structural insight into an anti-BRIL Fab as a G-protein-coupled receptor crystallization chaperone.
Authors: Miyagi, H. / Suzuki, M. / Yasunaga, M. / Asada, H. / Iwata, S. / Saito, J.I.
History
DepositionMay 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG LIGHT CHAIN
H: IGG HEAVY CHAIN
X: Soluble cytochrome b562
A: IGG LIGHT CHAIN
B: IGG HEAVY CHAIN
Y: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)118,6986
Polymers118,6986
Non-polymers00
Water11,980665
1
L: IGG LIGHT CHAIN
H: IGG HEAVY CHAIN
X: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)59,3493
Polymers59,3493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-34 kcal/mol
Surface area23930 Å2
MethodPISA
2
A: IGG LIGHT CHAIN
B: IGG HEAVY CHAIN
Y: Soluble cytochrome b562


Theoretical massNumber of molelcules
Total (without water)59,3493
Polymers59,3493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-37 kcal/mol
Surface area24160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.828, 75.239, 152.231
Angle α, β, γ (deg.)90.000, 99.670, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-365-

HOH

21A-346-

HOH

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Components

#1: Antibody IGG LIGHT CHAIN


Mass: 23681.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody IGG HEAVY CHAIN


Mass: 23896.709 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein Soluble cytochrome b562 / Cytochrome b-562


Mass: 11771.204 Da / Num. of mol.: 2 / Mutation: M29W,H124I,R128L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 665 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.88 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 6000, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.1→48.64 Å / Num. obs: 57858 / % possible obs: 94.9 % / Redundancy: 2.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.049 / Rrim(I) all: 0.08 / Net I/σ(I): 10.8 / Num. measured all: 134803 / Scaling rejects: 35
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
2.1-2.162.30.6451014344890.5680.490.8151.594.7
9.15-48.642.50.01917877050.9970.0150.02444.290

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.31 Å48.63 Å
Translation6.31 Å48.63 Å

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Processing

Software
NameVersionClassification
Aimless0.5.21data scaling
PHASER2.6.1phasing
REFMAC5.8.0232refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M6T, 1F58

1m6t

1f58


Resolution: 2.1→42.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.323 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2684 2917 5 %RANDOM
Rwork0.2136 ---
obs0.2164 54939 94.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.47 Å2 / Biso mean: 53.416 Å2 / Biso min: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0 Å20.33 Å2
2--0.18 Å20 Å2
3---0.48 Å2
Refinement stepCycle: final / Resolution: 2.1→42.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8291 0 0 665 8956
Biso mean---40.6 -
Num. residues----1074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0138611
X-RAY DIFFRACTIONr_bond_other_d0.0360.0177645
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.64611736
X-RAY DIFFRACTIONr_angle_other_deg2.3821.57517917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.41351099
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96223.731402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.075151425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5391533
X-RAY DIFFRACTIONr_chiral_restr0.0520.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029654
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021725
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 194 -
Rwork0.339 4064 -
all-4258 -
obs--94.5 %
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)
14.93752.78180.89861.97470.68172.5289-0.01020.15420.0928-0.13290.1578-0.0422-0.04140.0422-0.14770.04880.00240.03760.08650.01310.0402-47.276-25.826212.1
22.2096-2.4325-1.54193.90522.60523.7380.17330.18490.0194-0.2716-0.16910.17790.0197-0.1531-0.00430.0880.0050.00620.19320.00250.0629-21.113-35.407190.111
32.6788-0.5468-1.70211.31651.48143.3043-0.127-0.0415-0.30060.14970.0398-0.10380.4472-0.03740.08730.0962-0.05070.00390.10070.02050.1382-51.397-47.947213.976
44.53471.0372-0.47936.1599-0.28011.5739-0.2017-0.1429-0.0022-0.13180.1871-0.082-0.07060.18920.01470.03550.04490.00040.1804-0.0030.0019-15.354-43.765202.156
52.7375-0.03532.25742.51970.42836.84090.0568-0.12970.1078-0.2725-0.00210.3318-0.0785-0.7712-0.05470.0873-0.0956-0.02830.30890.07750.2346-75.252-39.338213.536
63.6565-1.61740.10912.5843-0.07161.5817-0.0622-0.07310.21180.21590.05050.1805-0.0787-0.13130.01160.0329-0.00440.03270.0874-0.01330.0614-18.588-15.732163.945
72.09040.9072-1.0774.8675-3.07973.5009-0.0469-0.46450.07750.30020.0251-0.0380.09860.02910.02190.12430.00840.03020.4006-0.07420.0344-44.458-27.144182.994
83.05010.4278-1.40251.9763-1.06672.8689-0.0608-0.0037-0.11140.03570.00250.00150.1533-0.12230.05840.01810.00350.00760.0630.00260.012-14.296-37.288158.852
93.7408-1.8002-0.65474.98350.96372.4611-0.1186-0.4070.10480.12560.08290.19150.0898-0.16970.03560.0563-0.07420.01290.2282-0.01570.0359-51.776-34.383170.989
102.452-0.4740.75242.8906-0.73656.1408-0.0256-0.33740.24830.43840.0147-0.3932-0.38730.24780.01080.09610.012-0.00750.2065-0.01230.27719.164-29.535164.401
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION2L109 - 213
3X-RAY DIFFRACTION3H1 - 119
4X-RAY DIFFRACTION4H120 - 221
5X-RAY DIFFRACTION5X2 - 105
6X-RAY DIFFRACTION6A1 - 108
7X-RAY DIFFRACTION7A109 - 214
8X-RAY DIFFRACTION8B1 - 119
9X-RAY DIFFRACTION9B120 - 221
10X-RAY DIFFRACTION10Y2 - 105

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