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- PDB-6v3u: Crystal Structure of the NDM_FIM-1 like Metallo-beta-Lactamase fr... -

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Basic information

Entry
Database: PDB / ID: 6v3u
TitleCrystal Structure of the NDM_FIM-1 like Metallo-beta-Lactamase from Erythrobacter litoralis in the Mono-Zinc Form
ComponentsBeta-lactamase II
KeywordsHYDROLASE / Metallo beta lactamase / lactam antibiotics / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesErythrobacter litoralis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKim, Y. / Maltseva, N. / Mulligan, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
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 the NDM_FIM-1 like Metallo-beta-Lactamase from Erythrobacter litoralis in the Mono-Zinc Form
Authors: Kim, Y. / Maltseva, N. / Mulligan, R. / Endres, M. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase II
B: Beta-lactamase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,75912
Polymers52,0682
Non-polymers69110
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-123 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.043, 80.043, 72.502
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase II


Mass: 26033.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Erythrobacter litoralis (strain HTCC2594) (bacteria)
Strain: HTCC2594 / Gene: ELI_07580 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: Q2N9N3

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Non-polymers , 5 types, 67 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M HEPES pH 7.5, 10 % (w/v) isopropanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97914 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 30109 / % possible obs: 96.9 % / Redundancy: 9.6 % / Biso Wilson estimate: 50.84 Å2 / Rmerge(I) obs: 0.131 / Net I/σ(I): 19.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 1012 / CC1/2: 0.673 / % possible all: 65.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: The un-deposited structure of the same protein in the apo-form

Resolution: 2→44.61 Å / SU ML: 0.2827 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.2679
RfactorNum. reflection% reflection
Rfree0.2385 1461 4.89 %
Rwork0.2021 --
obs0.2039 29886 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 73.8 Å2
Refinement stepCycle: LAST / Resolution: 2→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 36 57 3305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693364
X-RAY DIFFRACTIONf_angle_d0.8364586
X-RAY DIFFRACTIONf_chiral_restr0.0517514
X-RAY DIFFRACTIONf_plane_restr0.0053600
X-RAY DIFFRACTIONf_dihedral_angle_d18.71921952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.38471150.35982015X-RAY DIFFRACTION69
2.07-2.150.30441210.29752816X-RAY DIFFRACTION95.51
2.15-2.250.34041580.28062938X-RAY DIFFRACTION99.49
2.25-2.370.37371420.2472908X-RAY DIFFRACTION99.03
2.37-2.520.28131640.21972927X-RAY DIFFRACTION99.2
2.52-2.710.28921330.23082955X-RAY DIFFRACTION99.32
2.71-2.980.28741400.24052967X-RAY DIFFRACTION99.58
2.98-3.420.26971710.22272907X-RAY DIFFRACTION99.84
3.42-4.30.22631380.18423001X-RAY DIFFRACTION99.75
4.3-44.610.19611790.17112991X-RAY DIFFRACTION99.53
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)
14.084761005970.469215173541.310162430483.54383720871.355687752084.66873824221-0.1743234660490.856173649275-0.199466685363-0.4798104684750.7597776412-0.797016576104-0.2729440660131.72416194465-0.5492196868360.557958097633-0.09454420629030.0998170867911.04840781768-0.267359944030.5873632417928.52530760646.13092887704-5.89411888581
24.52887662211-1.577063920352.942624862223.570425700563.250212177577.9500085057-0.5181717719020.0826826143970.389277161583-0.3560078097930.50198108779-0.318330703116-1.484968164091.17930145863-0.115920922270.684194962178-0.27354398780.1745788070460.886352980420.04063010732950.45323741041422.887545984914.4467212959-3.90670288481
37.104158524880.894079170789-1.260725556115.664628589922.451041582574.18961035911-0.01548909865040.8971803410640.538835298755-0.7245992736810.138067574859-0.187820125465-1.119709836940.112271671776-0.2016647483090.654239169389-0.03929234244210.02199076470370.4374112707230.08115588856590.42294808115212.163793492815.0168118697-2.66058623416
44.697373040742.341956811822.32269182023.962447016052.455120779528.546644435930.439791666778-0.251383234277-0.4384482575630.724648797387-0.0441009031095-0.1981192913420.448157568460.290218339721-0.3529635520110.480998127012-0.057444931178-0.04548281051950.3944049112890.01297327259520.44299648585819.12788155374.3812597533314.079605439
53.70708193524-0.7296101358071.367775898363.42377704461.247143900954.093535360520.758102223344-0.284104999639-0.7972897197830.723386102824-0.0848869732447-0.09654974306631.74026805939-0.2858361183460.5146880060821.02585809997-0.156552112171-0.2106340480240.5137061565790.08253330333890.53849585355232.038501693312.728021610741.5574218336
64.50644038498-0.9516486436182.246268475254.34486734293-1.608352695435.464190842690.228029955099-0.718028275476-0.2474661727890.599806671028-0.04874767026750.566906778549-0.00046342681418-1.125582880420.0693012266620.522788981955-0.06592944729560.04175511282650.7333054724280.04122202650740.52965985607524.948734173627.962515076738.7085884569
72.070124854880.4815991192481.540516594313.432863936472.201932850268.10920002588-0.2187080196640.675400624637-0.154211733887-0.1709035823380.2892274773550.09950127090630.0194717183720.3975309129770.006747800443870.447210948188-0.062926726259-0.001356510852160.5822356431350.003807037164030.55672258082532.867926056321.474984240621.8307715336
85.667126412133.24087272173-0.35625493178.471178908591.087466991283.35491015224-0.2478070609290.82247228627-0.381362154817-0.4659908330250.540930430233-1.278709837880.870002570810.5088153162740.2075174604450.580049504782-0.0680136322871-0.02538817830.749643994987-0.1228768303580.6577342909640.353525966619.781791261822.3265855176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 101 )
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 175 )
4X-RAY DIFFRACTION4chain 'A' and (resid 176 through 261 )
5X-RAY DIFFRACTION5chain 'B' and (resid 35 through 119 )
6X-RAY DIFFRACTION6chain 'B' and (resid 120 through 175 )
7X-RAY DIFFRACTION7chain 'B' and (resid 176 through 231 )
8X-RAY DIFFRACTION8chain 'B' and (resid 232 through 261 )

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