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- PDB-3iie: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pestis. -

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Basic information

Entry
Database: PDB / ID: 3iie
Title1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pestis.
Components1-deoxy-D-xylulose 5-phosphate reductoisomerase
KeywordsOXIDOREDUCTASE / structural genomics / IDP00499 / xylulose / reductoisomerase / Isoprene biosynthesis / Metal-binding / NADP / Center for Structural Genomics of Infectious Diseases / CSGID
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 / 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 speciesYersinia pseudotuberculosis YPIII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsOsipiuk, J. / Mulligan, R. / Stam, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Yersinia pestis.
Authors: Osipiuk, J. / Mulligan, R. / Stam, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionJul 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 6, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9966
Polymers86,8612
Non-polymers1354
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-41 kcal/mol
Surface area30860 Å2
MethodPISA
2
A: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
B: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
hetero molecules

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)173,99212
Polymers173,7224
Non-polymers2708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area10600 Å2
ΔGint-85 kcal/mol
Surface area58570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.460, 121.460, 86.923
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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: 43430.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis YPIII (bacteria)
Strain: CO92 / Gene: dxr, YPK_1070 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B1JQG4, 1-deoxy-D-xylulose-5-phosphate reductoisomerase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16 M magnesium chloride, 0.08 M Tris-HCl buffer, 24% PEG-4000, 20% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2009
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.21→49.8 Å / Num. all: 37344 / Num. obs: 37344 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 34.2
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2 / Num. unique all: 1791 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0054refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2C82

2c82


Resolution: 2.21→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 15.99 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.306 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1867 5 %RANDOM
Rwork0.179 ---
all0.182 37285 --
obs0.182 37285 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.45 Å2 / Biso mean: 38.873 Å2 / Biso min: 17.55 Å2
Baniso -1Baniso -2Baniso -3
1-3.07 Å21.53 Å20 Å2
2--3.07 Å20 Å2
3----4.6 Å2
Refinement stepCycle: LAST / Resolution: 2.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5890 0 7 227 6124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226041
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.9748194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1395793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.05924.343251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.031151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.71545
X-RAY DIFFRACTIONr_chiral_restr0.1160.2974
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214487
X-RAY DIFFRACTIONr_mcbond_it0.7851.53911
X-RAY DIFFRACTIONr_mcangle_it1.45226305
X-RAY DIFFRACTIONr_scbond_it2.84432130
X-RAY DIFFRACTIONr_scangle_it4.5164.51882
LS refinement shellResolution: 2.21→2.268 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 124 -
Rwork0.273 2527 -
all-2651 -
obs-2651 97.71 %
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)
11.46930.6181-0.03640.63890.26981.15230.05850.0071-0.0622-0.1395-0.054-0.01260.07750.1257-0.00450.12920.0409-0.02380.07470.0120.029185.951557.70181.9473
23.5735-0.48711.68411.24010.32362.40250.1713-0.0701-0.30930.12450.1107-0.13180.38260.448-0.28210.10080.0563-0.07550.1719-0.00240.080394.570553.809612.0137
32.7904-0.05580.64960.45170.34861.0430.0272-0.1810.22850.0086-0.0604-0.0163-0.09040.03690.03330.0482-0.040.00610.0561-0.01690.024574.498668.506910.2461
42.71040.7516-1.80380.5033-1.24213.33140.0049-0.66640.1815-0.32060.03790.090.816-0.2777-0.04280.3528-0.2526-0.03650.4274-0.12070.139453.640253.00818.4709
53.5259-0.0785-0.30769.8578-4.68942.4057-0.0304-0.2154-0.4835-0.6624-0.0816-0.10590.5285-0.05440.1120.3595-0.15390.03040.15770.01290.070660.14244.264516.7687
61.26660.45210.73951.57080.50652.64080.0255-0.09020.05820.0118-0.01920.07140.0835-0.2078-0.00630.0309-0.05390.01280.0965-0.02180.011659.383862.90868.158
73.5254-0.7301-0.23191.21590.79921.29660.13210.17270.0095-0.0499-0.1046-0.038-0.0085-0.0398-0.02750.0526-0.0022-0.00930.05890.01570.006169.323760.165-4.6668
81.0033-0.02740.3960.56080.63532.38420.0669-0.3611-0.14340.1769-0.06210.03440.3965-0.1997-0.00470.1456-0.119-0.00810.25060.04490.032160.730854.782223.5994
90.556-0.69430.78431.6884-0.0692.513-0.1239-0.1373-0.02040.34890.17890.1857-0.0056-0.0588-0.05490.10930.01070.05490.0879-0.04250.154149.252286.6039-16.2428
101.4313-0.47551.13921.8177-0.80012.27680.0008-0.11660.08060.11730.08040.1972-0.0229-0.1792-0.08120.0784-0.01340.01280.0539-0.01240.153344.251394.2693-25.5371
111.3088-1.03860.14121.5313-0.05760.5140.03870.01030.24610.0493-0.0674-0.0355-0.0817-0.01710.02870.0428-0.02280.01740.02980.00050.089159.196786.0038-27.3618
122.2997-0.86980.24410.5813-0.74342.0772-0.1704-0.1220.04820.21690.0458-0.0423-0.31490.02990.12470.1503-0.0022-0.01380.02550.00740.0266.85270.8817-15.9539
130.71340.385-0.06541.58970.15160.7403-0.01710.02470.05970.0947-0.01670.24030.053-0.19690.03380.0239-0.02430.00660.06220.00140.041453.254259.1778-24.6201
140.5289-0.27730.04912.274-0.73120.94220.0303-0.11190.020.24890.08230.268-0.1802-0.2243-0.11260.10890.00560.03270.1067-0.00160.043254.548468.2679-8.158
150.90870.6705-0.11961.8865-0.74051.7893-0.08910.1705-0.0201-0.16870.11790.17730.1006-0.1765-0.02880.0356-0.0284-0.02160.0618-0.00770.036153.965558.5634-36.558
163.68592.7688-0.89084.0723-0.29050.9882-0.1710.61830.2526-0.51120.34880.17740.0733-0.074-0.17780.133-0.0325-0.04710.16980.05070.04857.664269.7071-45.8442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 25
2X-RAY DIFFRACTION2A26 - 87
3X-RAY DIFFRACTION3A88 - 176
4X-RAY DIFFRACTION4A177 - 197
5X-RAY DIFFRACTION5A198 - 227
6X-RAY DIFFRACTION6A228 - 261
7X-RAY DIFFRACTION7A262 - 299
8X-RAY DIFFRACTION8A300 - 395
9X-RAY DIFFRACTION9B1 - 26
10X-RAY DIFFRACTION10B27 - 70
11X-RAY DIFFRACTION11B71 - 145
12X-RAY DIFFRACTION12B146 - 180
13X-RAY DIFFRACTION13B181 - 261
14X-RAY DIFFRACTION14B262 - 307
15X-RAY DIFFRACTION15B308 - 366
16X-RAY DIFFRACTION16B367 - 396

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