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- PDB-1mq0: Crystal Structure of Human Cytidine Deaminase -

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Basic information

Entry
Database: PDB / ID: 1mq0
TitleCrystal Structure of Human Cytidine Deaminase
ComponentsCytidine Deaminase
KeywordsHYDROLASE / human / enzyme / cytidine deaminase / amine hydrolase / inhibitor / diazepinone / leukemia / chemotherapy / anticancer / drug / phi-phi interaction / edge-to-face interaction / protein
Function / homology
Function and homology information


negative regulation of nucleotide metabolic process / pyrimidine-containing compound salvage / cytidine deaminase / cellular response to external biotic stimulus / cytidine deamination / Pyrimidine salvage / cytidine deaminase activity / nucleoside binding / UMP salvage / cytosine metabolic process ...negative regulation of nucleotide metabolic process / pyrimidine-containing compound salvage / cytidine deaminase / cellular response to external biotic stimulus / cytidine deamination / Pyrimidine salvage / cytidine deaminase activity / nucleoside binding / UMP salvage / cytosine metabolic process / response to cycloheximide / negative regulation of cell growth / tertiary granule lumen / secretory granule lumen / ficolin-1-rich granule lumen / cell surface receptor signaling pathway / Neutrophil degranulation / protein homodimerization activity / zinc ion binding / extracellular region / identical protein binding / cytosol
Similarity search - Function
Cytidine deaminase, homotetrameric / : / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 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 ...Cytidine deaminase, homotetrameric / : / Cytidine and deoxycytidylate deaminase zinc-binding region / Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-BETA-RIBOFURANOSYL-1,3-DIAZEPINONE / Cytidine deaminase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChung, S.J. / Fromme, J.C. / Verdine, G.L.
CitationJournal: J.Med.Chem. / Year: 2005
Title: Structure of human cytidine deaminase bound to a potent inhibitor
Authors: Chung, S.J. / Fromme, J.C. / Verdine, G.L.
History
DepositionSep 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytidine Deaminase
B: Cytidine Deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6376
Polymers31,0212
Non-polymers6154
Water1,11762
1
A: Cytidine Deaminase
B: Cytidine Deaminase
hetero molecules

A: Cytidine Deaminase
B: Cytidine Deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,27312
Polymers62,0434
Non-polymers1,2318
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_685-x+1,-y+3,z1
Buried area12040 Å2
ΔGint-219 kcal/mol
Surface area16250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)52.398, 55.680, 90.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is a tetramer, and there is a dimer in the asymmetric unit. The other dimer of the tetramer can be obtained by the following symmetry operation: (-X, -Y,Z) dx=1 dy=3 dz=0

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Components

#1: Protein Cytidine Deaminase / Cytidine aminohydrolase


Mass: 15510.718 Da / Num. of mol.: 2 / Mutation: K27Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32320, cytidine deaminase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BRD / 1-BETA-RIBOFURANOSYL-1,3-DIAZEPINONE


Mass: 242.229 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N2O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: sodium acetate, 2-methyl-2,4-pentane-diol, calcium chloride, synthetic inhibitor, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
136.3 mg/mlprotein1drop
26.25 mMinhibitor1drop
35 mMbeta-mercaptoethanol1droppH7.5
4100 mM1dropNaCl
520 mMTris1drop
6100 mMsodium acetate1reservoirpH4.6
728-32 %MPD1reservoir
810 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 19, 2002 / Details: Osmic Blue
RadiationMonochromator: Nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→47.45 Å / Num. obs: 11082 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 4.58 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.56 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1134 / % possible all: 98.1
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. obs: 22165 / % possible obs: 97.1 % / Redundancy: 4.4 %
Reflection shell
*PLUS
% possible obs: 98.1 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.33

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Processing

Software
NameVersionClassification
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JTK

1jtk


Resolution: 2.4→47.45 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 210371.16 / Data cutoff high rms absF: 210371.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 520 4.9 %RANDOM
Rwork0.217 ---
all-10882 --
obs-10555 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.7547 Å2 / ksol: 0.338176 e/Å3
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1-19.15 Å20 Å20 Å2
2---7.11 Å20 Å2
3----12.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.4→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1922 0 36 62 2020
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it1.62
X-RAY DIFFRACTIONc_scangle_it2.242.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 83 4.8 %
Rwork0.289 1646 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA_REP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CDA_INHIBITOR.PARCDA_INHIBITOR.TOP
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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