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- PDB-4ooe: M. tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase W... -

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Basic information

Entry
Database: PDB / ID: 4ooe
TitleM. tuberculosis 1-deoxy-d-xylulose-5-phosphate reductoisomerase W203Y mutant bound to fosmidomycin and NADPH
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE/ANTIBIOTIC / reductoisomerase / OXIDOREDUCTASE-ANTIBIOTIC complex
Function / homology
Function and homology information


terpenoid biosynthetic process, mevalonate-independent / : / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / cobalt ion binding / NADPH binding / manganese ion binding / magnesium ion binding
Similarity search - Function
1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal / DXP reductoisomerase C-terminal domain / DXP reductoisomerase, C-terminal domain superfamily / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain / DXP reductoisomerase C-terminal domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A ...1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, N-terminal / 1-deoxy-D-xylulose 5-phosphate reductoisomerase, C-terminal / DXP reductoisomerase C-terminal domain / DXP reductoisomerase, C-terminal domain superfamily / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain / DXP reductoisomerase C-terminal domain / RNA polymerase sigma factor, region 2, helix turn helix motif / Rna Polymerase Sigma Factor; Chain: A / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID / : / Chem-NDP / : / 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.826 Å
AuthorsAllen, C.L. / Kholodar, S.A. / Murkin, A.S. / Gulick, A.M.
CitationJournal: Biochemistry / Year: 2014
Title: Alteration of the Flexible Loop in 1-Deoxy-d-xylulose-5-phosphate Reductoisomerase Boosts Enthalpy-Driven Inhibition by Fosmidomycin.
Authors: Kholodar, S.A. / Tombline, G. / Liu, J. / Tan, Z. / Allen, C.L. / Gulick, A.M. / Murkin, A.S.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
B: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
C: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
D: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,70916
Polymers169,7764
Non-polymers3,93412
Water30,1031671
1
A: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
B: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8558
Polymers84,8882
Non-polymers1,9676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-54 kcal/mol
Surface area26880 Å2
MethodPISA
2
C: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
D: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8558
Polymers84,8882
Non-polymers1,9676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-51 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.270, 114.240, 133.187
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
1-deoxy-D-xylulose 5-phosphate reductoisomerase / DXP reductoisomerase / 1-deoxyxylulose-5-phosphate reductoisomerase / 2-C-methyl-D-erythritol 4- ...DXP reductoisomerase / 1-deoxyxylulose-5-phosphate reductoisomerase / 2-C-methyl-D-erythritol 4-phosphate synthase


Mass: 42443.879 Da / Num. of mol.: 4 / Fragment: UNP residues 1-389 / Mutation: W203Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: dxr, RVBD_2870c / Production host: Escherichia coli (E. coli)
References: UniProt: I6YAH0, UniProt: P9WNS1*PLUS, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical
ChemComp-FOM / 3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID / FOSMIDOMYCIN


Mass: 183.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10NO5P / Comment: antibiotic*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1671 / 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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 6% PEG4000, 50 mM MES, 20% MPD, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.284 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 11, 2013
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.284 Å / Relative weight: 1
ReflectionResolution: 1.826→86.712 Å / Num. all: 151359 / Num. obs: 145456 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16
Reflection shellResolution: 1.826→1.93 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 3.8 / Num. unique all: 18847 / % possible all: 86.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A03

4a03


Resolution: 1.826→38.827 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 20.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 1949 1.37 %RANDOM
Rwork0.1697 ---
all0.1703 151777 --
obs0.1703 142154 93.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.826→38.827 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11020 0 240 1671 12931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711550
X-RAY DIFFRACTIONf_angle_d1.15315834
X-RAY DIFFRACTIONf_dihedral_angle_d16.4884088
X-RAY DIFFRACTIONf_chiral_restr0.0711865
X-RAY DIFFRACTIONf_plane_restr0.0052066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.826-1.87220.3387990.25577360X-RAY DIFFRACTION69
1.8722-1.92280.27471290.22319251X-RAY DIFFRACTION88
1.9228-1.97930.25991450.203710040X-RAY DIFFRACTION95
1.9793-2.04320.23481290.191310241X-RAY DIFFRACTION96
2.0432-2.11630.2261510.180810229X-RAY DIFFRACTION96
2.1163-2.2010.21611410.174210342X-RAY DIFFRACTION98
2.201-2.30110.19521410.172510287X-RAY DIFFRACTION97
2.3011-2.42240.21131470.171110417X-RAY DIFFRACTION98
2.4224-2.57420.22221500.178410347X-RAY DIFFRACTION97
2.5742-2.77290.21891450.17710303X-RAY DIFFRACTION96
2.7729-3.05180.22461400.173310390X-RAY DIFFRACTION97
3.0518-3.49320.21151470.161710392X-RAY DIFFRACTION97
3.4932-4.40010.17771420.140710343X-RAY DIFFRACTION95
4.4001-38.83610.17611430.150210263X-RAY DIFFRACTION92

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