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- PDB-7l6j: Crystal Structure of the Putative Hydrolase from Stenotrophomonas... -

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Basic information

Entry
Database: PDB / ID: 7l6j
TitleCrystal Structure of the Putative Hydrolase from Stenotrophomonas maltophilia
ComponentsPutative hydrolase
KeywordsHYDROLASE / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / putative hydrolase
Function / homologyisochorismatase activity / Isochorismatase / : / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / FORMIC ACID / Hydrolase
Function and homology information
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Functional and structural characterization of Stenotrophomonas maltophilia EntB, an unusual form of isochorismatase for siderophore synthesis.
Authors: Nas, M.Y. / Gabell, J. / Inniss, N. / Minasov, G. / Shuvalova, L. / Satchell, K.J.F. / Cianciotto, N.P.
History
DepositionDec 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jul 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,46714
Polymers24,0401
Non-polymers42713
Water7,476415
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.693, 171.693, 171.693
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

21A-644-

HOH

31A-681-

HOH

41A-683-

HOH

51A-709-

HOH

61A-740-

HOH

71A-784-

HOH

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Components

#1: Protein Putative hydrolase


Mass: 24040.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (strain K279a) (bacteria)
Strain: K279a / Gene: Smlt2820 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL-21 Magic / References: UniProt: B2FHQ4
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 4.4 Å3/Da / Density % sol: 72.06 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: Protein: 7.9 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen: ComPAS (H12), 3.0M Sodium formate; Cryo: 4.0M Sodium formate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 19, 2020 / Details: Be
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.78→30 Å / Num. obs: 41390 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Biso Wilson estimate: 18.8 Å2 / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.036 / Rrim(I) all: 0.117 / Rsym value: 0.111 / Χ2: 1.276 / Net I/σ(I): 23
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.886 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2047 / CC1/2: 0.851 / CC star: 0.959 / Rpim(I) all: 0.287 / Rrim(I) all: 0.931 / Rsym value: 0.886 / Χ2: 1.002 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.78→29.45 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.633 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1544 2031 4.9 %RANDOM
Rwork0.1374 ---
obs0.1382 39291 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.54 Å2 / Biso mean: 19.994 Å2 / Biso min: 12.37 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.78→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1676 0 24 466 2166
Biso mean--37.03 34.57 -
Num. residues----213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131821
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171670
X-RAY DIFFRACTIONr_angle_refined_deg1.3761.6572482
X-RAY DIFFRACTIONr_angle_other_deg0.3691.583837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8055230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.94919.098122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.57215268
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5991527
X-RAY DIFFRACTIONr_chiral_restr0.0590.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0530.022160
X-RAY DIFFRACTIONr_gen_planes_other0.0460.02449
LS refinement shellResolution: 1.78→1.826 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 149 -
Rwork0.217 2872 -
all-3021 -
obs--99.93 %
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)
12.487-0.4363-0.59141.25850.2222.40640.02740.13210.2793-0.0873-0.11590.0877-0.315-0.21140.08850.04940.0295-0.02560.03680.00580.072593.052419.953119.9531
20.65080.02010.06690.52550.27310.40640.01710.09740.0374-0.0307-0.05750.055-0.0232-0.08160.04040.01270.0126-0.00070.049-0.01470.022491.72825.897425.0346
30.78750.3020.54750.90590.93131.13490.0441-0.10870.03910.02-0.13730.0850.0175-0.20610.09320.0154-0.00210.01260.057-0.02790.02989.319910.24836.0979
40.916-0.18020.09582.51110.14271.03830.0004-0.02420.01170.01630.0155-0.17230.0344-0.0194-0.01590.0409-0.00360.00420.0206-0.01480.0219100.0043-2.947735.2304
50.58340.11290.08140.74230.40460.459-0.03490.11420.0552-0.02280.008-0.0002-0.0368-0.03150.02690.02610.0080.0030.0549-0.00440.023100.82068.025521.6844
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 19
2X-RAY DIFFRACTION2A20 - 87
3X-RAY DIFFRACTION3A88 - 128
4X-RAY DIFFRACTION4A129 - 141
5X-RAY DIFFRACTION5A142 - 210

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