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- PDB-6v70: Crystal Structure of Metallo Beta Lactamase from Hirschia baltica... -

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Basic information

Entry
Database: PDB / ID: 6v70
TitleCrystal Structure of Metallo Beta Lactamase from Hirschia baltica with Cadmium in the Active Site
ComponentsBeta-lactamase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / periplasmic space / response to antibiotic / zinc ion binding
Similarity search - Function
Beta-lactamases class B signature 1. / Beta-lactamase, class-B, conserved site / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / FORMIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesHirschia baltica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMaltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI) United States
CitationJournal: To Be Published
Title: Crystal Structure of Metallo Beta Lactamase from Hirschia baltica.
Authors: Maltseva, N. / Kim, Y. / Clancy, S. / Endres, M. / Mulligan, R. / Joachimiak, A.
History
DepositionDec 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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 / _struct_conn.ptnr2_symmetry
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,50111
Polymers25,8521
Non-polymers64910
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.352, 80.352, 245.373
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-302-

CL

21A-467-

HOH

31A-506-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Beta-lactamase


Mass: 25852.098 Da / Num. of mol.: 1 / Mutation: A257T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirschia baltica (strain ATCC 49814 / DSM 5838 / IFAM 1418) (bacteria)
Strain: ATCC 49814 / DSM 5838 / IFAM 1418 / Gene: Hbal_3075 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Gold / References: UniProt: C6XID6, beta-lactamase

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Non-polymers , 5 types, 116 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 20% PEG 8000; 0.1M TRIS pH 8.5; 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 14, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 22753 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 33.79 Å2 / Rsym value: 0.091 / Net I/σ(I): 22.4
Reflection shellResolution: 1.95→1.98 Å / Mean I/σ(I) obs: 1.88 / Num. unique obs: 1121 / CC1/2: 0.658 / Rsym value: 0.74

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6V54

6v54


Resolution: 1.95→33.47 Å / SU ML: 0.1972 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.5337
RfactorNum. reflection% reflection
Rfree0.1832 1102 4.84 %
Rwork0.1661 --
obs0.167 22752 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.97 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1670 0 7 106 1783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881750
X-RAY DIFFRACTIONf_angle_d1.02112382
X-RAY DIFFRACTIONf_chiral_restr0.0612264
X-RAY DIFFRACTIONf_plane_restr0.0057309
X-RAY DIFFRACTIONf_dihedral_angle_d18.218628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.040.25881220.22122658X-RAY DIFFRACTION99.64
2.04-2.140.2581390.19172682X-RAY DIFFRACTION100
2.14-2.280.21651370.17382661X-RAY DIFFRACTION100
2.28-2.450.18331410.17342685X-RAY DIFFRACTION100
2.45-2.70.18981320.17132692X-RAY DIFFRACTION100
2.7-3.090.22251350.17912728X-RAY DIFFRACTION100
3.09-3.890.19561550.17222709X-RAY DIFFRACTION99.97
3.89-33.470.13681410.14392835X-RAY DIFFRACTION99.2
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)
12.78507582399-1.02534352729-0.7117790398334.085330335570.7873135052233.14076062097-0.00453296696840.1900586716290.0759461562602-0.1517840123090.00841699988514-0.205864321141-0.03709302909640.194852421611-0.01209957100960.175052060840.03991247909090.01757287660990.3573582507580.01851205158740.221993245501-7.48417888064-29.575138873-24.529717853
22.686090717441.911500784141.266593360813.609202759564.833306439897.92379427635-0.193910814335-0.135537258119-0.282630429470.3753149311030.147033485352-0.003360390348780.4503340494770.322841198938-0.02875580737580.2215701311520.1173346089550.01044098243250.3176844438210.007966074135980.249708140367-15.9806209196-32.7007835814-7.09678033897
30.1764819433061.277944777450.9406205186549.479751586287.576796987967.41228904560.160946048851-0.027382313324-0.0284150975359-0.00374502812527-0.4178140708310.09788444572560.335401912585-0.1212152371730.03477624512270.3153410167230.1086622583410.0148217890270.2868048641110.01191168831030.342723390836-18.8727556961-44.5919339296-18.7736065001
44.222333202132.26935531350.895365312282.67665610352-1.042998254722.900495998240.00628321897294-0.2016952356180.152848542090.1881791131030.02020572641310.230907818191-0.220237343014-0.17653772134-0.01895112741040.2447087280040.1239731330030.04376998354950.281167092948-0.01892900060570.263044418667-23.4379868139-27.0558621792-10.0060917503
58.177020765990.188958983823-2.456176439781.713084940490.4980388822293.151131804-0.07073067203540.5145892435920.257238789538-0.239738805901-0.007483571230760.254638166498-0.126869482189-0.3197971982730.03728953629140.2852284196490.0748891254275-0.03742580655070.4118872287680.03462902129670.349445996373-24.8252350658-23.9106719364-26.1061421257
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 165 through 259 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 57 )
3X-RAY DIFFRACTION3chain 'A' and (resid 58 through 72 )
4X-RAY DIFFRACTION4chain 'A' and (resid 73 through 113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 164 )

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