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- PDB-4efz: Crystal Structure of a hypothetical metallo-beta-lactamase from B... -

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Basic information

Entry
Database: PDB / ID: 4efz
TitleCrystal Structure of a hypothetical metallo-beta-lactamase from Burkholderia pseudomallei
ComponentsMetallo-beta-lactamase family protein
KeywordsHYDROLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


hydrogen sulfide metabolic process / sulfur dioxygenase activity / Hydrolases / glutathione metabolic process / hydrolase activity / metal ion binding
Similarity search - Function
Persulfide dioxygenase-like, MBL-fold metallo-hydrolase domain / : / Metallo-beta-lactamase superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable metallo-hydrolase BURPS1710b_2304
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of a hypothetical metallo-beta-lactamase from Burkholderia pseudomallei
Authors: Fairman, J.W. / Craig, T.K. / Staker, B.L. / Stewart, L.
History
DepositionMar 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 22, 2025Group: Structure summary / Category: audit_author / pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase family protein
B: Metallo-beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,92319
Polymers64,8592
Non-polymers1,06317
Water9,170509
1
B: Metallo-beta-lactamase family protein
hetero molecules

A: Metallo-beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,92319
Polymers64,8592
Non-polymers1,06317
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area5360 Å2
ΔGint-54 kcal/mol
Surface area22820 Å2
MethodPISA
2
A: Metallo-beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8177
Polymers32,4301
Non-polymers3886
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Metallo-beta-lactamase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,10512
Polymers32,4301
Non-polymers67611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.320, 83.500, 96.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKOWN

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Metallo-beta-lactamase family protein


Mass: 32429.666 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710b / Gene: BURPS1710b_2304 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3JRV4

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Non-polymers , 6 types, 526 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2 M ammonium sulfate, 100 mM BIS-TRIS pH 6.50, 20 mg/mL BupsA.15999.a.A1 PS00414, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 84994 / Num. obs: 83635 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.509 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 27.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.640.4814.340669603197.1
1.64-1.690.3865.3439880591897.6
1.69-1.740.3036.6638723575297.6
1.74-1.790.2478.1337759560397.9
1.79-1.850.18710.5736784546097.8
1.85-1.910.14113.6435416527298.3
1.91-1.980.10717.1134413512998
1.98-2.070.08421.3132942493098.7
2.07-2.160.06526.4831630473298.4
2.16-2.260.05729.8430338455598.7
2.26-2.390.04933.7728760433798.8
2.39-2.530.04238.1527243411899
2.53-2.70.03543.1325611388299.2
2.7-2.920.0349.9723822363199.3
2.92-3.20.02656.7722063338999.5
3.2-3.580.02262.719664304499.3
3.58-4.130.0268.3117222270299.5
4.13-5.060.01970.5214435230398.9
5.06-7.160.0268.3911343184399.8
7.160.02165.735227100493.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→41.757 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8761 / SU ML: 0.2 / σ(F): 1.36 / Phase error: 19.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 4167 4.98 %
Rwork0.1705 --
obs0.1719 83627 98.36 %
all-84994 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.856 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso max: 69.84 Å2 / Biso mean: 24.0045 Å2 / Biso min: 10.33 Å2
Baniso -1Baniso -2Baniso -3
1--3.8093 Å2-0 Å20 Å2
2---3.0897 Å2-0 Å2
3---6.899 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4413 0 58 509 4980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154568
X-RAY DIFFRACTIONf_angle_d1.6156206
X-RAY DIFFRACTIONf_chiral_restr0.11702
X-RAY DIFFRACTIONf_plane_restr0.008816
X-RAY DIFFRACTIONf_dihedral_angle_d12.0971641
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.29861340.23032571270597
1.6182-1.63720.25241150.20922622273797
1.6372-1.65720.25391360.20322584272098
1.6572-1.67820.23581400.19732584272497
1.6782-1.70030.24491290.19032610273998
1.7003-1.72360.26261450.19462620276598
1.7236-1.74820.25591450.18582540268598
1.7482-1.77430.21071270.18522624275198
1.7743-1.8020.21231290.17642647277698
1.802-1.83150.21681430.17212612275598
1.8315-1.86310.19141030.16672643274698
1.8631-1.8970.21991380.16412612275098
1.897-1.93350.21311480.15942621276998
1.9335-1.9730.21181240.16542629275398
1.973-2.01590.18581230.16252660278399
2.0159-2.06280.19261380.16222638277698
2.0628-2.11430.17751520.15762609276198
2.1143-2.17150.20961520.1582641279399
2.1715-2.23540.19871270.15822678280599
2.2354-2.30750.2211350.17032638277399
2.3075-2.390.20611530.16712646279999
2.39-2.48570.21511380.17092669280799
2.4857-2.59880.21031520.17252675282799
2.5988-2.73580.19491480.16582675282399
2.7358-2.90720.1961540.16862675282999
2.9072-3.13150.18481460.17262706285299
3.1315-3.44660.20921380.1762724286299
3.4466-3.9450.16511440.16532731287599
3.945-4.96890.14951580.14172737289599
4.9689-41.77150.20631530.20292839299298
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)
11.9060.1272-0.15331.35540.15081.096-0.01110.05490.0626-0.1181-0.0052-0.2277-0.01780.08920.00740.08840.01830.02030.10420.01730.124160.863424.814112.4667
21.7432-0.62370.25955.21772.17334.2509-0.06480.0817-0.0349-0.136-0.05440.2151-0.0222-0.25670.09140.1234-0.00320.03690.13310.02190.135955.973537.03130.129
33.26844.2617-3.90897.6708-7.08586.5471-0.03540.34050.4127-0.1010.49590.6009-0.1111-0.6328-0.44450.20550.028-0.00850.1905-0.00350.199748.257944.71536.7264
44.4181.3261-3.18090.99720.26934.7912-0.125-0.4466-0.15390.0281-0.0405-0.17940.20290.24870.19530.06590.0066-0.00640.13620.00720.077948.192427.10328.537
51.47480.3876-0.07152.18270.15830.78030.0250.0432-0.0398-0.1292-0.0584-0.33320.00770.02810.03260.11350.00320.03860.10670.03110.111860.916774.351916.0829
62.4545-1.34173.46673.50441.25268.4740.2234-0.21270.00780.18070.0051-0.38570.2062-0.1966-0.23460.1551-0.0242-0.05780.13760.03760.274369.024466.227527.6462
70.63560.11570.2391.20460.33351.31820.1061-0.2018-0.13270.3143-0.1056-0.43980.09260.0465-0.00380.1876-0.0461-0.09130.15730.07030.259266.963359.438529.1156
85.70470.3837-0.79071.9461.69641.70420.01060.13130.0817-0.0537-0.0237-0.03830.1355-0.0679-0.00360.1039-0.00840.02920.12360.00340.051943.189370.215417.2902
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:172)A1 - 172
2X-RAY DIFFRACTION2(chain A and resid 173:238)A173 - 238
3X-RAY DIFFRACTION3(chain A and resid 239:263)A239 - 263
4X-RAY DIFFRACTION4(chain A and resid 264:294)A264 - 294
5X-RAY DIFFRACTION5(chain B and resid 1:154)B1 - 154
6X-RAY DIFFRACTION6(chain B and resid 163:177)B163 - 177
7X-RAY DIFFRACTION7(chain B and resid 178:257)B178 - 257
8X-RAY DIFFRACTION8(chain B and resid 258:294)B258 - 294

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