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- PDB-5w0u: Crystal structure of MBP fused activation-induced cytidine deamin... -

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Basic information

Entry
Database: PDB / ID: 5w0u
TitleCrystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with dCMP
Components
  • DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3')
  • DNA (5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3')
  • Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
KeywordsHYDROLASE/DNA / Class switch recombination / Cytidine deaminase / HYDROLASE-DNA complex
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
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / DNA / DNA (> 10) / 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: 2.9 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
DepositionMay 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
D: DNA (5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3')
G: DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3')
A: Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,56311
Polymers130,6464
Non-polymers9177
Water362
1
B: Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
D: DNA (5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3')
G: DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4907
Polymers68,9863
Non-polymers5054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0734
Polymers61,6601
Non-polymers4133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.005, 39.777, 153.935
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number3
Space group name H-MP121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase / MBP / MMBP / Maltodextrin-binding protein / Activation-induced cytidine deaminase / AID / Cytidine ...MBP / MMBP / Maltodextrin-binding protein / Activation-induced cytidine deaminase / AID / Cytidine aminohydrolase


Mass: 61659.883 Da / Num. of mol.: 2 / Fragment: UNP residues 27-392,UNP 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

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DNA chain , 2 types, 2 molecules DG

#2: DNA chain DNA (5'-D(*GP*TP*TP*CP*AP*AP*GP*GP*CP*CP*AP*G)-3')


Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*TP*GP*GP*CP*CP*TP*TP*GP*AP*AP*C)-3')


Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 5 types, 9 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Zn
#5: Chemical ChemComp-DCM / 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE / Deoxycytidine monophosphate


Mass: 307.197 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C9H14N3O7P
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1 M MES at pH 6.2, 3%PEG3350, 10 mM CaCl2, 20mM dCMP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→153.935 Å / Num. obs: 36653 / % possible obs: 98.3 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.1
Reflection shellResolution: 2.94→3.07 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3868 / CC1/2: 0.974 / Rpim(I) all: 0.313 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W0R

5w0r


Resolution: 2.9→153.935 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2814 1345 3.93 %
Rwork0.2509 --
obs0.2521 34208 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→153.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8595 483 50 2 9130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069410
X-RAY DIFFRACTIONf_angle_d0.73912864
X-RAY DIFFRACTIONf_dihedral_angle_d23.0213442
X-RAY DIFFRACTIONf_chiral_restr0.0521369
X-RAY DIFFRACTIONf_plane_restr0.0041576
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-3.00370.43861320.3793212334498
3.0037-3.1240.39831330.36443246337999
3.124-3.26610.42281340.36633239337398
3.2661-3.43840.37711360.34193219335599
3.4384-3.65380.35121320.29493271340399
3.6538-3.93590.2981350.27133294342999
3.9359-4.3320.29741330.2373262339598
4.332-4.95890.23561360.20953339347599
4.9589-6.24780.26891370.22833321345899
6.2478-154.15180.19621370.20213460359798

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