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- PDB-6mh4: Crystal Structure of 1-deoxy-D-xylulose-5-phosphate reductoisomer... -

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Basic information

Entry
Database: PDB / ID: 6mh4
TitleCrystal Structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase from Staphylococcus schleiferi, Apoenzyme
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE / reductoisomerase / staphylococci / MEP pathway / fosmidomycin / GlpT
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / NADPH binding / isomerase activity / metal 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
1-deoxy-D-xylulose 5-phosphate reductoisomerase
Similarity search - Component
Biological speciesStaphylococcus schleiferi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLee, S.G. / Jez, J.M.
CitationJournal: Plos Pathog. / Year: 2020
Title: Potent, specific MEPicides for treatment of zoonotic staphylococci.
Authors: Edwards, R.L. / Heueck, I. / Lee, S.G. / Shah, I.T. / Miller, J.J. / Jezewski, A.J. / Mikati, M.O. / Wang, X. / Brothers, R.C. / Heidel, K.M. / Osbourn, D.M. / Burnham, C.D. / Alvarez, S. / ...Authors: Edwards, R.L. / Heueck, I. / Lee, S.G. / Shah, I.T. / Miller, J.J. / Jezewski, A.J. / Mikati, M.O. / Wang, X. / Brothers, R.C. / Heidel, K.M. / Osbourn, D.M. / Burnham, C.D. / Alvarez, S. / Fritz, S.A. / Dowd, C.S. / Jez, J.M. / Odom John, A.R.
History
DepositionSep 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
B: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1699
Polymers84,4972
Non-polymers6727
Water1,45981
1
A: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules

B: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1699
Polymers84,4972
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area4760 Å2
ΔGint-111 kcal/mol
Surface area31070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.368, 71.368, 318.815
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Space group name HallP312(x,y,z+1/3)
Components on special symmetry positions
IDModelComponents
11B-277-

ARG

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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: 42248.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus schleiferi (bacteria) / Gene: dxr, SSCHL_1510 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0K1A7V6, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2000 mM ammonium sulfate, 100 mM sodium citrate/ citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2017
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→44.38 Å / Num. obs: 50897 / % possible obs: 99.2 % / Redundancy: 6.9 % / Net I/σ(I): 33.9
Reflection shellResolution: 2.15→2.23 Å / Num. unique obs: 5069

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Cootmodel building
HKL-3000data collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→44.38 Å / SU ML: 0.244 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.58
RfactorNum. reflection% reflection
Rfree0.2304 2581 5.07 %
Rwork0.1974 --
obs0.1991 50893 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 64.5575835149 Å2
Refinement stepCycle: LAST / Resolution: 2.15→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5830 0 35 81 5946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01572381492685965
X-RAY DIFFRACTIONf_angle_d1.060505986778068
X-RAY DIFFRACTIONf_chiral_restr0.0592226640475932
X-RAY DIFFRACTIONf_plane_restr0.007056455164051030
X-RAY DIFFRACTIONf_dihedral_angle_d3.528489610813612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1502409711-2.19160.29621310.26662495X-RAY DIFFRACTION93.2528409091
2.1916-2.23630.26861490.24672689X-RAY DIFFRACTION99.7890295359
2.2363-2.2850.31541460.24722650X-RAY DIFFRACTION99.7502675705
2.285-2.33810.280921360.24862636X-RAY DIFFRACTION99.604743083
2.3381-2.39660.2991620.24632678X-RAY DIFFRACTION100
2.3966-2.46140.32461510.24262696X-RAY DIFFRACTION99.9648876404
2.4614-2.53380.26341390.24352675X-RAY DIFFRACTION99.7518610422
2.5338-2.61560.26151260.22872680X-RAY DIFFRACTION99.609513667
2.6156-2.7090.271470.23482667X-RAY DIFFRACTION99.7518610422
2.709-2.81750.25791480.231232700X-RAY DIFFRACTION99.8597475456
2.8175-2.94570.30291610.22342665X-RAY DIFFRACTION99.6122664787
2.9457-3.10090.27141640.2272674X-RAY DIFFRACTION99.2654774397
3.1009-3.29520.25491350.22082667X-RAY DIFFRACTION99.4675186368
3.2952-3.54950.20251250.20382711X-RAY DIFFRACTION99.1955229101
3.5495-3.90650.23461540.18642685X-RAY DIFFRACTION99.2310380986
3.9065-4.47130.2061340.16072741X-RAY DIFFRACTION99.4465582843
4.4713-5.63160.1861330.17082751X-RAY DIFFRACTION99.5169082126
5.6316-44.380.18261400.1742852X-RAY DIFFRACTION99.5011639508
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.116724005040.03911639220640.04281276002613.20634579031-1.873297309256.68234392440.153722830918-0.1837500019790.2373577407590.0961834304039-0.0980318459120.0173264819355-0.6496850216870.58413491014-0.03241686786180.343078714889-0.1012698596530.03879531131010.362202210995-0.08867754347890.322524028603-12.225528069717.1344200295-39.7805038832
22.591383291170.26488904549-2.310996916071.08443404103-0.4831813257422.5066285888-0.0497354510994-0.233441754158-0.0862113472654-0.120079806085-0.220496774213-0.1714987677240.1470316848750.3572611297870.2362942718120.277051151588-0.0172887839155-0.04031407108520.5838564710550.09167827812720.412688706446-7.31835594427-5.23089387178-35.529488544
33.16112165526-1.01911641961.440443054245.66087420154-1.754793403125.294849534090.282771369176-1.051876386270.04784932557721.17524276376-0.3041054067390.159608752839-0.0246321251819-0.5034238361340.05464121173160.588150441023-0.145686785383-0.01125647944931.15500787374-0.07583617827980.40674979204536.1718192505-6.115594610757.83721393588
42.4684132096-0.879748871604-0.2679039365712.887159292141.497925999512.55869356872-0.209634851724-1.79703712005-0.0367134993021.501867229740.1087922388380.621734988545-0.428012712936-1.04557714057-0.1704149654341.09925718644-0.04819047443170.2512333999611.59968977493-0.07999665308320.71830653077125.2537322344-2.4147740057715.218690852
53.970125948770.102118260483-0.969765903912.79336508476-0.9210501547994.364646017290.135209788522-0.452641194520.5590810567360.276747660661-0.004399208605860.513512221324-0.640498698857-0.804481165953-0.06600453635360.4611298534940.09330627593380.01935709946220.798835541765-0.04168490168090.57681615194529.53550993111.8549363835-7.8072296062
62.92493427981.04003369118-0.5201950798362.9952326711-0.7931037254532.31831675636-0.04986620204780.093082298912-0.1162928129440.02387775508470.07073846204790.2880445221910.22232733246-0.3339836463-0.06657382505660.312240336016-0.0254233433461-0.02321911462560.7524942658910.02294380346040.47318769508430.8353391441-12.3383722192-22.3881649907
73.26180022950.258706961482-0.6696824740291.604675648640.2588165262821.516928985530.0354808625985-0.691748755237-0.2610728933490.192079715011-0.0668099919379-0.06323366503280.340829430699-0.3931270790830.08864076247760.436830900281-0.0283072564675-0.01545781933660.8209855696180.08039598869770.48910436802342.2866162214-12.4115305542-17.219519121
86.62362529693-2.76490244608-0.5893813367085.41191836023-0.5800986924242.52553202525-0.3221943474970.194531270643-0.6890515378460.04431094811650.2875717038380.5554050866650.654229926948-0.9139939055610.0522869531920.43536948277-0.1123474562030.01694838393281.090632404090.05533203833750.50587094152515.3347491024-16.4615227636-17.7010616654
96.72698814578-1.504663995751.026885179946.354810117331.311936539452.532911118-0.494512593507-0.6057087730580.5933094471981.124592379760.3382748820420.774770961604-0.105433917297-0.8069233142570.04776825058590.3859081911230.1384166512590.08179130511061.353067846360.1216810010220.5667265421339.05990926747-5.83740099909-10.0858031865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 374 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 58 )
4X-RAY DIFFRACTION4chain 'B' and (resid 59 through 83 )
5X-RAY DIFFRACTION5chain 'B' and (resid 84 through 158 )
6X-RAY DIFFRACTION6chain 'B' and (resid 159 through 255 )
7X-RAY DIFFRACTION7chain 'B' and (resid 256 through 299 )
8X-RAY DIFFRACTION8chain 'B' and (resid 300 through 350 )
9X-RAY DIFFRACTION9chain 'B' and (resid 351 through 374 )

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