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- PDB-1gu9: Crystal Structure of Mycobacterium tuberculosis Alkylperoxidase AhpD -

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Basic information

Entry
Database: PDB / ID: 1gu9
TitleCrystal Structure of Mycobacterium tuberculosis Alkylperoxidase AhpD
ComponentsALKYLHYDROPEROXIDASE D
KeywordsOXIDOREDUCTASE / ALKYLHYDROPEROXIDASE / TUBERCULOSIS
Function / homologyAhpD-like / AhpD-like / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsNunn, C.M. / Djordjevic, S. / Hillas, P.J. / Nishida, C. / Ortiz de Montellano, P.R.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: The Crystal Structure of Mycobacterium Tuberculosis Alkylhydroperoxidase Ahpd, a Potential Target for Antitubercular Drug Design
Authors: Nunn, C.M. / Djordjevic, S. / Hillas, P.J. / Nishida, C. / Ortiz de Montellano, P.R.
History
DepositionJan 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Advisory / Database references / Structure summary
Category: audit_author / citation_author / pdbx_unobs_or_zero_occ_residues
Item: _audit_author.name / _citation_author.name
Revision 1.4Oct 9, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALKYLHYDROPEROXIDASE D
B: ALKYLHYDROPEROXIDASE D
C: ALKYLHYDROPEROXIDASE D
D: ALKYLHYDROPEROXIDASE D
E: ALKYLHYDROPEROXIDASE D
F: ALKYLHYDROPEROXIDASE D
G: ALKYLHYDROPEROXIDASE D
H: ALKYLHYDROPEROXIDASE D
I: ALKYLHYDROPEROXIDASE D
J: ALKYLHYDROPEROXIDASE D
K: ALKYLHYDROPEROXIDASE D
L: ALKYLHYDROPEROXIDASE D


Theoretical massNumber of molelcules
Total (without water)227,30612
Polymers227,30612
Non-polymers00
Water15,259847
1
A: ALKYLHYDROPEROXIDASE D
B: ALKYLHYDROPEROXIDASE D
C: ALKYLHYDROPEROXIDASE D


Theoretical massNumber of molelcules
Total (without water)56,8273
Polymers56,8273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: ALKYLHYDROPEROXIDASE D
E: ALKYLHYDROPEROXIDASE D
F: ALKYLHYDROPEROXIDASE D


Theoretical massNumber of molelcules
Total (without water)56,8273
Polymers56,8273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
G: ALKYLHYDROPEROXIDASE D
H: ALKYLHYDROPEROXIDASE D
I: ALKYLHYDROPEROXIDASE D


Theoretical massNumber of molelcules
Total (without water)56,8273
Polymers56,8273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
J: ALKYLHYDROPEROXIDASE D
K: ALKYLHYDROPEROXIDASE D
L: ALKYLHYDROPEROXIDASE D


Theoretical massNumber of molelcules
Total (without water)56,8273
Polymers56,8273
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)186.377, 117.280, 88.986
Angle α, β, γ (deg.)90.00, 113.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
ALKYLHYDROPEROXIDASE D


Mass: 18942.205 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 847 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsRESIDUE 104 IN ALL CHAINS WAS FOUND TO BE A METHIONINE FROM A PATTERSON AND SUBSEQUENT REFINEMENT

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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: 1.97 Å3/Da / Density % sol: 37 %
Crystal growpH: 6
Details: 100MM SODIUM CITRATE BUFFER, PH 5.6, CONTAINING 200MM AMMONIUM ACETATE AND 26% PEG 4000. MIXED IN EQUAL VOLUME WITH AHPD (4.5 MG/ML) IN 25 MM MOPS BUFFER, PH 7.2, CONTAINING 50 MM KCL, 10% GLYCEROL, 0.1MM EDTA
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMsodium citrate1reservoirpH5.6
2200 mMammonium acetate1reservoir
326 %PEG40001reservoir
44.5 mg/mlprotein1drop
525 mMMOPS1droppH7.2
650 mM1dropKCl
710 %glycerol1drop
80.1 mMEDTA1drop
95.0 mMdithiothreitol1drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.88550,0.918400,0.978900 , 0.97877
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2001 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.88551
20.91841
30.97891
40.978771
ReflectionResolution: 1.9→30 Å / Num. obs: 136927 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 7.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.75 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 500 Å / Num. measured all: 1263412
Reflection shell
*PLUS
% possible obs: 99.3 %

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Processing

Software
NameVersionClassification
CNS1refinement
HKLdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→29.6 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.313 13434 9.8 %RANDOM
Rwork0.243 ---
obs0.243 136435 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9056 Å2 / ksol: 0.349187 e/Å3
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å20.36 Å2
2---0.91 Å20 Å2
3----1.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15327 0 0 847 16174
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.00922
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3408
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.70926
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91609
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it11.0881.5
X-RAY DIFFRACTIONc_mcangle_it11.2952
X-RAY DIFFRACTIONc_scbond_it11.9572
X-RAY DIFFRACTIONc_scangle_it13.3992.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3937 1360 10 %
Rwork0.3176 12042 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CN_PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMPROTEIN_BREAK.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 500 Å / Rfactor Rfree: 0.31
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg18.70926
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91609

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