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- PDB-1kll: Molecular basis of mitomycin C resictance in streptomyces: Crysta... -

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Basic information

Entry
Database: PDB / ID: 1kll
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
1,2-CIS-1-HYDROXY-2,7-DIAMINO-MITOSENE / Mitomycin-binding protein
Similarity search - Component
Biological speciesStreptomyces lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / 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 12, 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: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mitomycin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8922
Polymers14,5721
Non-polymers3201
Water2,756153
1
A: mitomycin-binding protein
hetero molecules

A: mitomycin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7844
Polymers29,1442
Non-polymers6412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5550 Å2
ΔGint-24 kcal/mol
Surface area11100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.751, 60.458, 44.077
Angle α, β, γ (deg.)90.00, 106.78, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the crystallographic two fold axis

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Components

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


Mass: 14571.889 Da / Num. of mol.: 1 / Mutation: L19M, L25M
Source method: isolated from a genetically manipulated source
Details: complexed with 2,7-DIAMINOMITOSENE, residue MC / Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL221(DE3) / References: UniProt: O05205
#2: Chemical ChemComp-MC / 1,2-CIS-1-HYDROXY-2,7-DIAMINO-MITOSENE / CARBAMIC ACID 2,6-DIAMINO-1-HYDROXY-5-METHYL-4,7-DIOXO-2,3,4,7-TETRAHYDRO-1H-3A-AZA-CYCLOPENTA[A]INDEN-8-YLMETHYL ESTER


Mass: 320.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H16N4O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: ammonium sulfate, MES buffer, beta-octylglucoside, pH 6.0, VAPOR DIFFUSION, HANGING DROP at 298K, VAPOR DIFFUSION, HANGING DROP, 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 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 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→25 Å / Num. obs: 18054 / % possible obs: 99.9 % / Redundancy: 3.64 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 12.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 4 / Num. unique all: 1776 / % possible all: 100
Reflection
*PLUS
Num. measured all: 66770 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.301

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Processing

Software
NameClassification
SHELXSphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: AB INITIO / Resolution: 1.5→10 Å / Cross valid method: FREE R / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1349 5 %RANDOM
Rwork0.131 ---
obs0.124 17993 99.6 %-
all-18054 --
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 37 153 2147
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d2.14
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.124 / Rfactor Rfree: 0.209 / Rfactor Rwork: 0.136
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.14

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