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- PDB-9zmu: Crystal structure of an Iole protein from Brucella melitensis (he... -

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Basic information

Entry
Database: PDB / ID: 9zmu
TitleCrystal structure of an Iole protein from Brucella melitensis (hexagonal 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: 1.98 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 (hexagonal 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
Water39622
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)47.806, 47.806, 492.577
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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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.: 22 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
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-0613, 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: 1.98→492.58 Å / Num. obs: 25281 / % possible obs: 100 % / Redundancy: 34.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.227 / Rpim(I) all: 0.039 / Rrim(I) all: 0.23 / Χ2: 1.45 / Net I/σ(I): 21.1 / Num. measured all: 866595
Reflection shellResolution: 1.98→2.03 Å / % possible obs: 100 % / Redundancy: 35.5 % / Rmerge(I) obs: 2.542 / Num. measured all: 62289 / Num. unique obs: 1757 / CC1/2: 0.539 / Rpim(I) all: 0.428 / Rrim(I) all: 2.579 / Χ2: 0.88 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(2.0_5765: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→41.4 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2939 1302 5.19 %
Rwork0.2498 --
obs0.2521 25085 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→41.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 1 22 2351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082381
X-RAY DIFFRACTIONf_angle_d0.8473220
X-RAY DIFFRACTIONf_dihedral_angle_d14.032872
X-RAY DIFFRACTIONf_chiral_restr0.05354
X-RAY DIFFRACTIONf_plane_restr0.008427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.060.43521350.372514X-RAY DIFFRACTION100
2.06-2.150.37251330.33732551X-RAY DIFFRACTION100
2.15-2.270.34751500.30472570X-RAY DIFFRACTION100
2.27-2.410.37771310.3022583X-RAY DIFFRACTION100
2.41-2.590.34141590.30262569X-RAY DIFFRACTION100
2.59-2.860.30671470.27822622X-RAY DIFFRACTION100
2.86-3.270.31421450.27372642X-RAY DIFFRACTION100
3.27-4.120.28641440.22352741X-RAY DIFFRACTION100
4.12-41.40.22961580.19922991X-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)
10.0717-0.0550.09270.4908-0.4180.4222-0.2356-0.22940.26080.5810.0483-0.1182-0.56380.0105-0.14560.1715-0.01210.01580.4192-0.12740.319510.59524.0943-11.6287
20.20360.0001-0.10380.0763-0.09660.09350.1588-0.00990.0126-0.20090.00150.198-0.1756-0.0459-00.3213-0.0416-0.03470.3979-0.08680.400415.677228.8873-12.4102
30.0734-0.1043-0.05680.11370.24360.33990.07980.07530.1488-0.1033-0.1061-0.0523-0.10640.014600.2982-0.0450.02670.3825-0.06710.358415.881123.2227-27.0171
40.54420.56890.54151.15330.43470.5635-0.35930.34460.1002-0.35230.020.6130.0904-0.4619-0.08690.3334-0.002-0.06550.5038-0.47520.254-4.49911.7035-23.4417
50.1204-0.10050.07780.4484-0.03350.0764-0.13520.00680.0324-0.1363-0.01640.17420.1738-0.0143-0.01660.2595-0.07570.04270.4282-0.13010.271410.93399.6457-30.1022
60.2857-0.2118-0.0420.6803-0.39510.44030.36990.1881-0.4586-0.5471-0.65880.2318-0.24720.4338-0.0420.3804-0.00520.05750.4956-0.17020.416511.98481.8119-28.3292
70.0150.114-0.1140.9-1.0231.2493-0.06640.253-0.42540.1019-0.2398-0.0331-0.14670.0937-0.19940.2618-0.07920.09660.3955-0.21170.40339.44175.9193-16.1983
80.16030.00960.3190.06580.08790.7704-0.04440.3575-0.17080.2062-0.21680.374-0.2018-0.1474-0.64640.2424-0.00910.11930.3472-0.19540.48.29375.3649-12.5297
90.16790.26-0.04110.4783-0.23660.33010.083-0.1017-0.05670.2374-0.20060.06770.0596-0.0691-0.06970.26920.00520.00110.3153-0.13690.28722.179312.52-6.8821
100.16640.13640.2610.13450.1230.21140.2802-0.1579-0.07750.0335-0.08260.1529-0.1096-0.09860.00510.2437-0.02620.02430.3056-0.12350.390116.154411.9112-9.7536
110.13360.11890.11210.13270.03710.0838-0.0158-0.27860.3233-0.00790.2088-0.08910.08830.11550.00340.3052-0.056-0.02140.2961-0.14760.351620.023313.8728-2.7003
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 49 )
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 104 )
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 124 )
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 161 )
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 176 )
7X-RAY DIFFRACTION7chain 'A' and (resid 177 through 191 )
8X-RAY DIFFRACTION8chain 'A' and (resid 192 through 222 )
9X-RAY DIFFRACTION9chain 'A' and (resid 223 through 246 )
10X-RAY DIFFRACTION10chain 'A' and (resid 247 through 275 )
11X-RAY DIFFRACTION11chain 'A' and (resid 276 through 298 )

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