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- PDB-9bzb: Crystal structure of metallo-hydrolase-like_MBL-fold protein from... -

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Basic information

Entry
Database: PDB / ID: 9bzb
TitleCrystal structure of metallo-hydrolase-like_MBL-fold protein from Salmonella typhimurium LT2
Componentsputative metallo beta lactamase
KeywordsHYDROLASE / putative Zn-dependent hydrolase / metallo-hydrolase-like_MBL-fold / CSBID / Structural Genomics / Center for Structural Biology of Infectious Diseases
Function / homologyMetallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / hydrolase activity / FORMIC ACID / Zn-dependent hydrolase
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of metallo-hydrolase-like_MBL-fold protein from Salmonella typhimurium LT2
Authors: Kim, Y. / Maltseva, N. / Endres, M. / Joachimiak, A.
History
DepositionMay 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative metallo beta lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2864
Polymers30,0821
Non-polymers2043
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.831, 120.831, 35.339
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z

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Components

#1: Protein putative metallo beta lactamase / Zn-dependent hydrolase


Mass: 30082.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Gene: STM3737 / Plasmid: p53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q8ZL44
#2: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 50 mM Tris pH 7.6. 2.9 % (v/v) PEG350 MME, 34.3 % (v/v) PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 21268 / % possible obs: 97.7 % / Redundancy: 7.7 % / Biso Wilson estimate: 45.06 Å2 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.048 / Rrim(I) all: 0.147 / Net I/σ(I): 20.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.837 / Mean I/σ(I) obs: 0.92 / Num. unique obs: 803 / CC1/2: 0.616 / Rpim(I) all: 0.518 / Rrim(I) all: 0.99 / % possible all: 75.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→39.55 Å / SU ML: 0.3155 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.6335
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2357 1074 5.13 %
Rwork0.1967 19846 -
obs0.1987 20920 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.35 Å2
Refinement stepCycle: LAST / Resolution: 1.95→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 12 39 2137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272200
X-RAY DIFFRACTIONf_angle_d0.56942997
X-RAY DIFFRACTIONf_chiral_restr0.0434334
X-RAY DIFFRACTIONf_plane_restr0.0047395
X-RAY DIFFRACTIONf_dihedral_angle_d13.9065809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.040.36581000.33581875X-RAY DIFFRACTION74.03
2.04-2.150.33831440.27322376X-RAY DIFFRACTION93.68
2.15-2.280.2991480.25792558X-RAY DIFFRACTION99.63
2.28-2.460.34651310.23692580X-RAY DIFFRACTION100
2.46-2.710.30481060.26712601X-RAY DIFFRACTION99.89
2.71-3.10.26351520.23322568X-RAY DIFFRACTION99.93
3.1-3.90.21171400.19392614X-RAY DIFFRACTION99.93
3.9-39.550.19441530.14992674X-RAY DIFFRACTION99.86
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)
14.37998465373-2.19485000877-1.106793676183.388975844941.199659181293.86105359734-0.00170700984143-0.0826977773018-0.258373695601-0.4861946209570.325896115468-0.137834516232-0.8011972371430.242650800141-0.3583807784290.541096337449-0.03009834496730.05197756073840.461651825269-0.1304872860860.375547242326-14.0880197046-31.978474855810.5294411455
23.189749576530.557510897705-0.2847390692441.218607495830.01533734263044.581624448010.054161867170.3792521116150.258741229857-0.09080468718750.537855254159-0.530373074115-0.4255538895920.934855750349-0.5287825386240.434992376894-0.1822184627150.06429709587630.809549494858-0.2723227689570.5853175387620.676669515462-39.3302303087-1.93619940016
34.82446560883-0.318837204195-1.06461236030.1283536267840.5200620890911.868930184660.03984241757920.2219246466940.663048668837-0.1655197007110.36917087842-0.413532736422-0.7886412546050.719534943294-0.5101533950710.574660171493-0.2456653486050.0954976561140.588398744692-0.05042932341410.473304543283-5.22034377519-34.6136639453-6.39599568713
43.6082759906-0.0313528725957-1.226453091372.101044934361.699643039016.02935978228-0.07455598497180.5393025452590.171554379707-0.3405594152890.305495200461-0.0874566289517-0.714605448961-0.0176433325875-0.2417625428080.390290094536-0.0996083942018-0.01396114213080.4369988184070.007283522652240.338961382533-16.4544828332-37.3575263452-5.76416841695
54.00548795819-0.6027606862430.8412336819563.3773853340.7228842666573.341373254060.007896137832490.0557015344184-0.08784964029490.08930778947730.24959438253-0.1543724204260.01180424458440.0475522257279-0.1970158487750.316966186488-0.0419489371673-0.04531010205990.31633623594-0.01903239808120.283085068636-17.5891080112-45.30359541543.0162096604
66.77760868744-1.87128937344-1.050119646431.312039498640.7289396888714.08727617520.0392714210136-0.092065530158-0.4829453025540.05122581403230.33395276606-0.2065292364230.2891094601130.353779046569-0.313233918420.436619659488-0.0259203463768-0.04978872473070.344989949309-0.09114359437970.44740639698-14.5669882744-50.91177279985.1013476638
75.897601177-0.4982890550531.130276276882.764677780051.433609999446.948642255710.03647055007110.162418044117-0.7697377845460.4792698392540.50066002505-0.8002685796130.637195161311.94197480044-0.4873042883190.7267767565170.241797832865-0.1679337349471.00270573607-0.3234273836830.6223184838784.34879454217-51.78493719758.8271636479
89.05296754838-2.35868027601-3.139356920947.066410014293.297141490212.222437411530.351529088732-0.591481554742-0.31757285050.823271926086-0.322227812688-0.1582804921340.931374633560.0141845331842-0.04407308578470.560379199152-0.0516594929216-0.0644406882050.5006792137260.04572906792340.416311754155-18.5627782672-51.440453229414.2497495269
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 21 through 47 )21 - 471 - 27
22chain 'A' and (resid 48 through 93 )48 - 9328 - 73
33chain 'A' and (resid 94 through 124 )94 - 12474 - 104
44chain 'A' and (resid 125 through 180 )125 - 180105 - 160
55chain 'A' and (resid 181 through 222 )181 - 222161 - 202
66chain 'A' and (resid 223 through 251 )223 - 251203 - 231
77chain 'A' and (resid 252 through 271 )252 - 271232 - 251
88chain 'A' and (resid 272 through 290 )272 - 290252 - 270

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