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- PDB-5w0z: Crystal structure of MBP fused activation-induced cytidine deamin... -

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Basic information

Entry
Database: PDB / ID: 5w0z
TitleCrystal structure of MBP fused activation-induced cytidine deaminase (AID)
ComponentsMBP fused activation-induced cytidine deaminase
KeywordsHYDROLASE / Class switch recombination / Cytidine deaminase
Function / homology
Function and homology information


somatic diversification of immunoglobulins / regulation of nuclear cell cycle DNA replication / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of DNA methylation-dependent heterochromatin formation / isotype switching ...somatic diversification of immunoglobulins / regulation of nuclear cell cycle DNA replication / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of DNA methylation-dependent heterochromatin formation / isotype switching / DNA demethylation / carbohydrate transmembrane transporter activity / somatic hypermutation of immunoglobulin genes / B cell differentiation / Chromatin modifications during the maternal to zygotic transition (MZT) / P-body / mRNA processing / outer membrane-bounded periplasmic space / defense response to virus / cellular response to lipopolysaccharide / defense response to bacterium / ubiquitin protein ligase binding / protein-containing complex / RNA binding / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
APOBEC-like, N-terminal / APOBEC-like N-terminal domain / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. ...APOBEC-like, N-terminal / APOBEC-like N-terminal domain / APOBEC/CMP deaminase, zinc-binding / Cytidine and deoxycytidylate deaminases zinc-binding region signature. / Cytidine and deoxycytidylate deaminase domain / Cytidine and deoxycytidylate deaminases domain profile. / Cytidine deaminase-like / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Single-stranded DNA cytosine deaminase
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.61 Å
AuthorsQiao, Q. / Wang, L. / Wu, H.
CitationJournal: Mol. Cell / Year: 2017
Title: AID Recognizes Structured DNA for Class Switch Recombination.
Authors: Qiao, Q. / Wang, L. / Meng, F.L. / Hwang, J.K. / Alt, F.W. / Wu, H.
History
DepositionJun 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: MBP fused activation-induced cytidine deaminase
A: MBP fused activation-induced cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,5674
Polymers123,4362
Non-polymers1312
Water0
1
A: MBP fused activation-induced cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7832
Polymers61,7181
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MBP fused activation-induced cytidine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7832
Polymers61,7181
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.680, 167.650, 188.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 0 / Auth seq-ID: 3 - 1181 / Label seq-ID: 3 - 549

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

#1: Protein MBP fused activation-induced cytidine deaminase


Mass: 61717.914 Da / Num. of mol.: 2
Fragment: UNP P0AEY0 residues 27-392,UNP Q9GZX7 residues 13-181
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, AICDA, AID / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P0AEY0, UniProt: Q9GZX7, single-stranded DNA cytosine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.26 M NaCl, 0.1 M MES pH 6.0, 12% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.6→188.3 Å / Num. obs: 12574 / % possible obs: 99.8 % / Redundancy: 7.9 % / Net I/σ(I): 6.4
Reflection shellResolution: 3.61→3.74 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 11572 / CC1/2: 0.688 / Rpim(I) all: 0.743 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W0R

5w0r


Resolution: 3.61→25 Å / Cor.coef. Fo:Fc: 0.855 / Cor.coef. Fo:Fc free: 0.821 / SU B: 60.783 / SU ML: 0.85 / Cross valid method: THROUGHOUT / ESU R Free: 0.967 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30693 672 5.1 %RANDOM
Rwork0.2743 ---
obs0.27601 12574 88.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.687 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.1 Å20 Å2
3----0.28 Å2
Refinement stepCycle: 1 / Resolution: 3.61→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8534 0 2 0 8536
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028752
X-RAY DIFFRACTIONr_bond_other_d0.0040.028222
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.94811876
X-RAY DIFFRACTIONr_angle_other_deg1.115318902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02851068
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63424.126412
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.722151428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2151548
X-RAY DIFFRACTIONr_chiral_restr0.0620.21264
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219960
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022068
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2526.3734296
X-RAY DIFFRACTIONr_mcbond_other2.2526.3724295
X-RAY DIFFRACTIONr_mcangle_it4.1219.5465356
X-RAY DIFFRACTIONr_mcangle_other4.129.5485357
X-RAY DIFFRACTIONr_scbond_it1.8686.5964456
X-RAY DIFFRACTIONr_scbond_other1.8686.5974456
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4649.796520
X-RAY DIFFRACTIONr_long_range_B_refined6.96151.3619899
X-RAY DIFFRACTIONr_long_range_B_other6.96151.3679900
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 65678 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 3.61→3.702 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 21 -
Rwork0.348 389 -
obs--39.12 %

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