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- PDB-1kmz: MOLECULAR BASIS OF MITOMYCIN C RESICTANCE IN STREPTOMYCES: CRYSTA... -

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Basic information

Entry
Database: PDB / ID: 1kmz
TitleMOLECULAR BASIS OF MITOMYCIN C RESICTANCE IN STREPTOMYCES: CRYSTAL STRUCTURES OF THE MRD PROTEIN WITH AND WITHOUT A DRUG DERIVATIVE
Componentsmitomycin-binding protein
KeywordsANTIMICROBIAL PROTEIN / Mitomycin C / antibiotic resistance / SAD / anomalous diffraction / domain swapping / p-staking
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
Mitomycin-binding protein
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsMartin, T.W. / Dauter, Z. / Devedjiev, Y. / Sheffield, P. / Jelen, F. / He, M. / Sherman, D. / Otlewski, J. / Derewenda, Z.S. / Derewenda, U.
CitationJournal: Structure / Year: 2002
Title: Molecular basis of mitomycin C resistance in streptomyces: structure and function of the MRD protein.
Authors: Martin, T.W. / Dauter, Z. / Devedjiev, Y. / Sheffield, P. / Jelen, F. / He, M. / Sherman, D.H. / Otlewski, J. / Derewenda, Z.S. / Derewenda, U.
History
DepositionDec 17, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mitomycin-binding protein


Theoretical massNumber of molelcules
Total (without water)14,3951
Polymers14,3951
Non-polymers00
Water3,063170
1
A: mitomycin-binding protein

A: mitomycin-binding protein


Theoretical massNumber of molelcules
Total (without water)28,7902
Polymers28,7902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556-x+1/2,y+1/2,-z+11
2
A: mitomycin-binding protein

A: mitomycin-binding protein


Theoretical massNumber of molelcules
Total (without water)28,7902
Polymers28,7902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3260 Å2
ΔGint-21 kcal/mol
Surface area11270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)44.508, 60.651, 43.776
Angle α, β, γ (deg.)90.00, 105.97, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the crystallographyc two fold axis

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Components

#1: Protein mitomycin-binding protein / Mrd / Mitomycin resistance protein D


Mass: 14395.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL221(DE3) / References: UniProt: O05205
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 1.7 Å3/Da / Density % sol: 37.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: ammonium sulfate, MES buffer, beta-octylglucoside, pH 6.0, VAPOR DIFFUSION at 298K, temperature 298.0K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
13 mg/mlprotein11
255 %ammonium sulfate11
3100 mMMES11pH6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.97
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 24, 2000 / Details: MIRRORS
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 17820 / % possible obs: 99.9 % / Redundancy: 4.15 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.034
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.33 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. measured all: 74125 / Rmerge(I) obs: 0.034
Reflection shell
*PLUS
% possible obs: 99.4 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementStarting model: PDB ENTRY 1KLL

1kll


Resolution: 1.5→10 Å / Cross valid method: FREE R / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1478 9 %RANDOM
obs0.163 -99.9 %-
all-16273 --
Refine analyzeLuzzati coordinate error obs: 0.15 Å / Num. disordered residues: 5
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms982 0 0 170 1152
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d1.8
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.163 / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.8

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