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- PDB-4zn6: X-ray Crystal Structure of 1-deoxy-D-xylulose 5-phosphate reducto... -

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Basic information

Entry
Database: PDB / ID: 4zn6
TitleX-ray Crystal Structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (IspC) from Acinetobacter baumannii
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE / SSGCID / IspC / 1-deoxy-D-xylulose 5-phosphate reductoisomerase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / 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 speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: to be published
Title: X-ray Crystal Structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (IspC) from Acinetobacter baumannii
Authors: Fairman, J.W. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMay 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
B: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6047
Polymers88,1912
Non-polymers4125
Water11,115617
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-53 kcal/mol
Surface area29770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.270, 65.430, 121.680
Angle α, β, γ (deg.)90.000, 92.090, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN

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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: 44095.648 Da / Num. of mol.: 2 / Fragment: AcbaC.01136.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (strain AB307-0294) (bacteria)
Strain: AB307-0294 / Gene: dxr, ABBFA_001475 / Plasmid: AcbaC.01136.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B7H1U5, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 617 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4549.75
2
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: MCSG1 screen C8: 0.2 M ammonium sulfate, 0.1 M sodium citrate:HCl pH 5.60, 25% PEG 4000
PH range: 5.6

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
22
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 21, 2015
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 53531 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 21.43 Å2 / Rmerge F obs: 0.995 / Rmerge(I) obs: 0.096 / Rrim(I) all: 0.112 / Χ2: 0.983 / Net I/σ(I): 10.23 / Num. measured all: 197745
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.05-2.10.7990.5063.0214766395039360.5999.6
2.1-2.160.8640.4183.5614356384738170.48899.2
2.16-2.220.8940.3474.2913992376537360.40599.2
2.22-2.290.9230.2915.0213461363036080.34199.4
2.29-2.370.9490.2355.9813066353135140.27699.5
2.37-2.450.9580.2066.5412581340033960.24299.9
2.45-2.540.970.1737.5712166329732840.20399.6
2.54-2.650.9790.1448.6211725317831650.16999.6
2.65-2.760.9810.1269.7811225304330380.14899.8
2.76-2.90.9840.10511.3110670289828960.12399.9
2.9-3.060.9880.09312.4210242278727790.10999.7
3.06-3.240.9920.07814.239642263526270.09299.7
3.24-3.470.9920.0715.698972246924640.08299.8
3.47-3.740.9920.06218.168303229422890.07399.8
3.74-4.10.9940.05619.057695214321360.06599.7
4.1-4.580.9940.05419.956984193919260.06499.3
4.58-5.290.9960.04920.126256170117000.05799.9
5.29-6.480.9960.04718.645336145014490.05599.9
6.48-9.170.9980.03821.034132113811380.045100
9.170.9980.02921.5421756496330.03597.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ANM

3anm


Resolution: 2.05→41.755 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 2007 3.75 %RANDOM
Rwork0.1717 51503 --
obs0.1733 53510 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.86 Å2 / Biso mean: 25.1179 Å2 / Biso min: 10.23 Å2
Refinement stepCycle: final / Resolution: 2.05→41.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5781 0 23 617 6421
Biso mean--37.35 32.61 -
Num. residues----780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045948
X-RAY DIFFRACTIONf_angle_d0.8048117
X-RAY DIFFRACTIONf_chiral_restr0.036993
X-RAY DIFFRACTIONf_plane_restr0.0041051
X-RAY DIFFRACTIONf_dihedral_angle_d12.9892139
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10130.30411400.239536473787100
2.1013-2.15810.26721420.20843657379999
2.1581-2.22160.25341370.19063639377699
2.2216-2.29330.22421470.17753659380699
2.2933-2.37520.20611430.173636573800100
2.3752-2.47030.21091410.181436543795100
2.4703-2.58270.25571450.176936983843100
2.5827-2.71890.23121440.18136593803100
2.7189-2.88920.22381400.185436623802100
2.8892-3.11220.22341440.187836693813100
3.1122-3.42520.26281440.174837063850100
3.4252-3.92060.19851470.153636863833100
3.9206-4.93820.15081430.136137193862100
4.9382-41.76350.18761500.16137913941100
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)
10.6349-0.22-0.12241.81931.28962.5937-0.05230.0109-0.09980.05740.0326-0.06810.1818-0.04850.02230.1482-0.00840.00050.11690.00160.16917.3367-31.814416.327
20.65610.5190.6461.02660.46980.9584-0.00110.0890.0004-0.0056-0.00690.06970.0021-0.0045-0.00270.12710.0094-0.00810.15540.01210.20165.3222-9.480613.2285
33.33850.1912-0.94280.59430.09621.04290.0156-0.0757-0.0886-0.0993-0.0342-0.0820.07840.1563-0.00530.14760.0119-0.01220.14790.02350.128728.8002-6.937111.1734
40.6533-0.1807-0.62670.54430.26851.49820.0050.08080.0058-0.04980.029-0.03940.0336-0.0094-0.04060.1125-0.0051-0.02020.13140.00130.160621.5745-6.449310.3769
50.6696-0.07150.07381.7859-0.38281.3192-0.0416-0.06290.02440.24280.05530.09-0.2436-0.1793-0.00690.19190.04650.00290.1829-0.00550.15315.104125.085845.3977
60.3112-0.0130.30490.6055-0.04972.1738-0.0176-0.1164-0.01690.19750.0271-0.025-0.10520.1837-0.00960.20170.0146-0.01210.189-0.00090.146519.96395.648148.7221
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 98 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 99 through 185 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 246 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 247 through 406 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 10 through 159 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 160 through 406 )B0

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