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- PDB-2a4w: Crystal Structure Of Mitomycin C-Binding Protein Complexed with C... -

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Basic information

Entry
Database: PDB / ID: 2a4w
TitleCrystal Structure Of Mitomycin C-Binding Protein Complexed with Copper(II)-Bleomycin A2
ComponentsMitomycin-Binding Protein
KeywordsANTIMICROBIAL PROTEIN / alfa/beta protein / Mitomycin C-binding protein / Copper(II)-Bleomycin A2 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
BLEOMYCIN A2 / COPPER (II) ION / Mitomycin-binding protein
Similarity search - Component
Biological speciesStreptomyces caespitosus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDanshiitsoodol, N. / de Pinho, C.A. / Matoba, Y. / Kumagai, T. / Sugiyama, M.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: The Mitomycin C (MMC)-binding Protein from MMC-producing Microorganisms Protects from the Lethal Effect of Bleomycin: Crystallographic Analysis to Elucidate the Binding Mode of the Antibiotic to the Protein
Authors: Danshiitsoodol, N. / de Pinho, C.A. / Matoba, Y. / Kumagai, T. / Sugiyama, M.
History
DepositionJun 30, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 18, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitomycin-Binding Protein
B: Mitomycin-Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4134
Polymers30,9332
Non-polymers1,4802
Water6,233346
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-43 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.390, 60.670, 48.240
Angle α, β, γ (deg.)90.00, 101.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Mitomycin-Binding Protein


Mass: 15466.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces caespitosus (bacteria) / Gene: mrd / Plasmid: pET-mrd / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O05205*PLUS
#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-BLM / BLEOMYCIN A2 / N1-[3-(DIMETHYLSULFONIO)-PROPYL]BLEOMYCINAMIDE


Mass: 1416.560 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H85N17O21S3 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN WHICH DERIVES FROM STREPTOMYCES CAESPITOSUS DOES NOT ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN WHICH DERIVES FROM STREPTOMYCES CAESPITOSUS DOES NOT CURRENTLY EXIST. THE 8 C-TERMINAL RESIDUES WERE HIS TAGS.

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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: 2.07 Å3/Da / Density % sol: 40.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG8000, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→26.38 Å / Num. all: 114525 / Num. obs: 40048 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.86 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.71 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4029 / % possible all: 100

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
CrystalCleardata reduction
CrystalCleardata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KLL

1kll


Resolution: 1.5→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1935 5 %RANDOM
Rwork0.205 ---
obs0.205 38513 96 %-
all-38513 --
Displacement parametersBiso mean: 15 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2021 0 97 346 2464
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_improper_angle_d0.73
X-RAY DIFFRACTIONx_mcbond_it1.111.5
X-RAY DIFFRACTIONx_mcangle_it1.742
X-RAY DIFFRACTIONx_scbond_it2.042
X-RAY DIFFRACTIONx_scangle_it3.172.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 290 4.7 %
Rwork0.352 5901 -
obs-5800 92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramtophcsdx.pro.top
X-RAY DIFFRACTION2bleo-5.paramtoph19.sol
X-RAY DIFFRACTION3bleo-4.top

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