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- PDB-9zmv: Crystal structure of an Iole protein from Brucella melitensis (or... -

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Basic information

Entry
Database: PDB / ID: 9zmv
TitleCrystal structure of an Iole protein from Brucella melitensis (orthorhombic P form)
ComponentsIole protein
KeywordsBIOSYNTHETIC PROTEIN / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE
Function / homologyIolE/MocC family / : / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / : / Iole protein
Function and homology information
Biological speciesBrucella melitensis biotype 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of an Iole protein from Brucella melitensis (orthorhombic P form)
Authors: Liu, L. / Lovell, S. / Battaile, K.P.
History
DepositionDec 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iole protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1312
Polymers34,0771
Non-polymers551
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.015, 64.086, 101.834
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 Iole protein


Mass: 34076.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biotype 1 (strain ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M) (bacteria)
Strain: ATCC 23456 / CCUG 17765 / NCTC 10094 / 16M / Gene: BMEII0570 / Plasmid: BrmeA.18154.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8YCG0
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MPH D1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2-Propanol, 20 mM 1,4-Butanediol and 20 mM ...Details: MPH D1: 20%(v/v) PEG 500 MME, 10%(w/v) PEG 20000, 100 mM Imidazole/MES, pH 6.5, 20 mM 1,6-Hexanediol, 20 mM 1-Butanol, 20 mM 1,2-Propanediol, 20 mM 2-Propanol, 20 mM 1,4-Butanediol and 20 mM 1,3-Propanediol. BrmeA.18154.a.B2.PW39413 at 8 mg/mL. plate 20332 D1 drop 1, Puck: PSL-0614, Cryo: direct

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 3, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.1→48.01 Å / Num. obs: 19031 / % possible obs: 100 % / Redundancy: 7.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.08 / Rrim(I) all: 0.227 / Χ2: 0.99 / Net I/σ(I): 7.5 / Num. measured all: 150860
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 1.279 / Num. measured all: 12909 / Num. unique obs: 1544 / CC1/2: 0.583 / Rpim(I) all: 0.467 / Rrim(I) all: 1.363 / Χ2: 0.98 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.0_5904: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→43.43 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 905 4.77 %
Rwork0.1899 --
obs0.1918 18982 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→43.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 1 151 2490
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042396
X-RAY DIFFRACTIONf_angle_d0.5563242
X-RAY DIFFRACTIONf_dihedral_angle_d14.953878
X-RAY DIFFRACTIONf_chiral_restr0.041356
X-RAY DIFFRACTIONf_plane_restr0.005430
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.27341490.24312966X-RAY DIFFRACTION100
2.23-2.40.27911340.22412978X-RAY DIFFRACTION100
2.4-2.650.29641530.21912951X-RAY DIFFRACTION100
2.65-3.030.25931580.2052996X-RAY DIFFRACTION100
3.03-3.810.20281540.1813012X-RAY DIFFRACTION100
3.82-43.430.18541570.15913174X-RAY DIFFRACTION100
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)
14.2034-0.776-0.64085.8994-0.33272.0315-0.07960.1858-0.4769-0.0237-0.0555-0.02950.02920.0720.12290.227-0.0135-0.00670.2377-0.02720.1196-7.907210.0402-10.5451
25.7827-0.41710.28745.13721.18883.44870.03480.2139-0.4209-0.0776-0.20640.14290.3449-0.15660.13850.1507-0.0122-0.00290.18350.00640.1692-12.00455.032-9.6947
31.5568-0.3746-1.32891.0375-0.34884.2020.18650.0382-0.075-0.1614-0.03810.0494-0.0051-0.0755-0.14430.2198-0.0069-0.02190.1413-0.04820.195-12.21575.8444-21.0906
41.45210.9991-1.95662.3973-0.83993.738-0.04490.3278-0.1071-0.29050.11660.07080.2113-0.2902-0.06140.20710.0356-0.02380.2295-0.03350.214-12.82347.5594-29.5817
55.5367-0.10522.8164.21210.72744.5707-0.04350.14470.2294-0.1318-0.0916-0.2676-0.05310.45130.14310.20440.05320.08280.33950.06570.3058.507617.8404-25.0905
62.75110.5813-0.04752.57060.72362.45220.0180.16940.1708-0.3912-0.0359-0.0603-0.36290.03770.03450.18270.03890.00710.16270.0160.143-7.094518.6834-31.9311
71.43180.74151.77042.15711.27684.1892-0.0447-0.15190.0602-0.2664-0.1374-0.1331-0.4498-0.13730.17610.23640.02160.01090.1980.04410.2712-6.521126.354-26.2502
85.13010.7511.2364.1978-1.83176.54170.08090.11970.4017-0.3356-0.19210.0085-0.2710.36420.11240.1790.03630.01430.1902-0.00150.2079-12.673228.6133-22.1831
96.38981.3625-2.72821.9337-0.73672.3132-0.48330.21870.0909-0.09540.2259-0.39220.03480.17270.15180.1706-0.03650.00060.27060.0890.3495.031426.2314-10.1468
104.4898-0.368-1.07433.20440.27883.8549-0.1594-0.03130.03860.1593-0.0348-0.0852-0.14390.30790.19480.1635-0.002-0.02220.15770.03730.14092.148821.7673-8.827
113.4525-0.32251.48071.3538-0.09942.43760.0805-0.106-0.0326-0.00470.01360.0695-0.0458-0.1035-0.08160.1646-0.02440.02210.15990.01720.1814-11.881122.1984-11.6452
122.991-2.05350.38417.1376-1.85453.75410.138-0.21720.12390.0415-0.01880.0623-0.1685-0.3103-0.1240.14570.01640.02040.259-0.01110.139-15.674922.3735-4.2752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 104 )
5X-RAY DIFFRACTION5chain 'A' and (resid 105 through 124 )
6X-RAY DIFFRACTION6chain 'A' and (resid 125 through 161 )
7X-RAY DIFFRACTION7chain 'A' and (resid 162 through 191 )
8X-RAY DIFFRACTION8chain 'A' and (resid 192 through 207 )
9X-RAY DIFFRACTION9chain 'A' and (resid 208 through 222 )
10X-RAY DIFFRACTION10chain 'A' and (resid 223 through 246 )
11X-RAY DIFFRACTION11chain 'A' and (resid 247 through 275 )
12X-RAY DIFFRACTION12chain 'A' and (resid 276 through 298 )

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