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- PDB-5zgq: Crystal structure of NDM-1 at pH7.5 (Tris-HCl, (NH4)2SO4) in comp... -

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Basic information

Entry
Database: PDB / ID: 5zgq
TitleCrystal structure of NDM-1 at pH7.5 (Tris-HCl, (NH4)2SO4) in complex with hydrolyzed ampicillin
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE/ANTIBIOTIC / NDM-1 / metallo-beta-lactamase / antibiotic resistent / conformational change / HYDROLASE-ANTIBIOTIC complex
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
Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HYDROXIDE ION / Chem-ZZ7 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsZhang, H. / Hao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31670753 China
CitationJournal: Antimicrob. Agents Chemother. / Year: 2018
Title: Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1.
Authors: Zhang, H. / Ma, G. / Zhu, Y. / Zeng, L. / Ahmad, A. / Wang, C. / Pang, B. / Fang, H. / Zhao, L. / Hao, Q.
History
DepositionMar 10, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 12, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo-beta-lactamase type 2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,29410
Polymers51,2642
Non-polymers1,0308
Water10,539585
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1475
Polymers25,6321
Non-polymers5154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1475
Polymers25,6321
Non-polymers5154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.200, 79.068, 134.162
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Metallo-beta-lactamase type 2 / B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta- ...B2 metallo-beta-lactamase / Beta-lactamase type II / Metallo-beta-lactamase NDM-1 / Metallo-beta-lactamase type II / New Delhi metallo-beta-lactamase-1 / NDM-1


Mass: 25631.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pRHisMBP / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: C7C422, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 367.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O5S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.35 % / Mosaicity: 0.352 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris-HCl pH7.5, 25% PEG 4000, 0.7M (NH4)2SO4, 20mg/ml ampicillin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 66725 / % possible obs: 98.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.081 / Χ2: 1.014 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.5-1.556.30.45763180.677195
1.55-1.626.20.38364000.71196.3
1.62-1.696.20.30365620.76197.9
1.69-1.786.20.2365850.82198.7
1.78-1.896.30.17366540.893199.1
1.89-2.046.40.12966781.092199.6
2.04-2.246.60.1167291.371199.8
2.24-2.566.80.0967821.444199.8
2.56-3.236.90.05368551.147199.9
3.23-507.10.03271621.0691100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6X

3q6x
PDB Unreleased entry


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.305 / SU ML: 0.038 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.061
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1536 3374 5.1 %RANDOM
Rwork0.118 ---
obs0.1198 63271 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 69.53 Å2 / Biso mean: 18.135 Å2 / Biso min: 10.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.17 Å2
Refinement stepCycle: final / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 56 585 4235
Biso mean--14.58 32.62 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193783
X-RAY DIFFRACTIONr_bond_other_d0.0020.023417
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.9475154
X-RAY DIFFRACTIONr_angle_other_deg0.9623.0037875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2145492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83524.534161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.23115565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1111518
X-RAY DIFFRACTIONr_chiral_restr0.0820.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214298
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02742
X-RAY DIFFRACTIONr_rigid_bond_restr0.92837192
X-RAY DIFFRACTIONr_sphericity_free26.075330
X-RAY DIFFRACTIONr_sphericity_bonded4.73157343
LS refinement shellResolution: 1.501→1.54 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.178 219 -
Rwork0.156 4401 -
all-4620 -
obs--94.13 %
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)
16.87540.8827-3.73781.85323.241910.0177-0.06120.1175-0.27540.39310.016-0.07880.9250.04620.04520.22740.1412-0.00750.21210.01210.01647.50193.623336.9301
29.2837-1.3811-4.7371.09790.718411.65050.35210.1179-0.3757-0.0977-0.1251-0.08630.65860.5645-0.22710.15070.0536-0.04270.0607-0.02260.100649.8998-1.557145.9058
36.33860.64332.55941.2460.36213.69520.00930.0744-0.1312-0.081-0.0053-0.12920.19480.0077-0.00390.13030.0190.0040.03380.0130.064249.9415.660748.3896
41.05530.15190.5491.1604-0.33152.57350.0745-0.0719-0.08590.0661-0.0235-0.04340.2474-0.002-0.0510.12090.0016-0.01410.05340.0090.053646.02336.461954.2574
50.6290.0774-0.010.8224-0.15070.4926-0.0177-0.11570.02130.05060-0.00560.0409-0.00340.01770.0780.0042-0.00460.0801-0.00120.051945.07422.184156.4704
61.175-0.19690.29181.4759-0.1870.8522-0.00160.051-0.0345-0.1271-0.0104-0.09770.06510.08390.0120.07830.00790.01610.08050.00130.052954.673821.531243.7273
72.6668-3.03651.34755.4644-1.82422.38040.13430.26620.1341-0.4635-0.2314-0.1906-0.04780.21440.09710.1123-0.00030.04460.0790.01150.047157.565625.304736.6921
810.5276-2.68743.21572.276-2.90843.7262-0.05030.20990.37360.373-0.091-0.1138-0.50780.09130.14130.22660.0854-0.05390.1045-0.02430.029533.414462.829839.9594
917.4131-0.40583.91862.37960.39497.4593-0.18940.08790.1291-0.18780.02410.255-0.9698-0.67980.16530.1530.1041-0.01090.08560.0120.068235.525768.021848.837
103.09520.2273-2.10630.732-0.01275.1224-0.04220.1490.1216-0.11470.03380.0397-0.0228-0.02640.00840.0877-0.0015-0.01490.0515-0.00120.07736.965460.66250.2246
110.4695-0.0457-0.03110.83330.51511.5451-0.0033-0.01330.0662-0.03060.0272-0.0008-0.0920.0325-0.02380.073-0.0039-0.00530.0691-0.00270.06643.467957.253154.2739
120.56680.19930.01880.70810.16620.36-0.002-0.0563-0.00770.01830.0011-0.0178-0.00640.03380.00080.07190.0029-0.00570.0749-0.00070.059343.712543.360457.4527
130.69440.0354-0.14891.20780.27531.0524-0.00230.03820.0295-0.1018-0.02410.1042-0.0197-0.06190.02640.06480.0012-0.01850.0896-0.01010.085130.145444.575148.2866
142.2696-2.0251-1.36944.9462.88555.80550.02290.2038-0.111-0.2839-0.16290.17420.243-0.22150.14010.0697-0.0089-0.01870.0711-0.02520.081724.588240.475244.0623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 39
2X-RAY DIFFRACTION2A40 - 48
3X-RAY DIFFRACTION3A49 - 67
4X-RAY DIFFRACTION4A68 - 112
5X-RAY DIFFRACTION5A113 - 197
6X-RAY DIFFRACTION6A198 - 253
7X-RAY DIFFRACTION7A254 - 270
8X-RAY DIFFRACTION8B30 - 39
9X-RAY DIFFRACTION9B40 - 48
10X-RAY DIFFRACTION10B49 - 68
11X-RAY DIFFRACTION11B69 - 129
12X-RAY DIFFRACTION12B130 - 201
13X-RAY DIFFRACTION13B202 - 254
14X-RAY DIFFRACTION14B255 - 270

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