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- PDB-5zgt: Crystal structure of NDM-1 at pH7.5 (HEPES) with 2 molecules per ... -

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Basic information

Entry
Database: PDB / ID: 5zgt
TitleCrystal structure of NDM-1 at pH7.5 (HEPES) with 2 molecules per asymmetric unit
ComponentsMetallo-beta-lactamase type 2
KeywordsHYDROLASE / NDM-1 / metallo-beta-lactamase / antibiotic resistent / conformational change
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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
HYDROXIDE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 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)51,83611
Polymers51,2642
Non-polymers5729
Water11,818656
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9646
Polymers25,6321
Non-polymers3325
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-58 kcal/mol
Surface area10550 Å2
MethodPISA
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8725
Polymers25,6321
Non-polymers2404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-59 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.691, 73.475, 66.461
Angle α, β, γ (deg.)90.000, 98.230, 90.000
Int Tables number4
Space group name H-MP1211

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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


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 656 / 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: 1.92 Å3/Da / Density % sol: 35.87 % / Mosaicity: 0.426 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97941 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 27, 2011
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 119756 / % possible obs: 99.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.06 / Χ2: 1.356 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.2-1.226.70.44459130.908198.9
1.22-1.246.70.39159080.912198.5
1.24-1.276.70.36259800.919198.9
1.27-1.296.80.3259350.921199.2
1.29-1.326.80.27759330.934198.9
1.32-1.356.80.24359800.945199.2
1.35-1.396.90.21659640.953199.6
1.39-1.426.90.19359800.997199.3
1.42-1.466.90.16859471.06199.5
1.46-1.516.90.14859791.169199.3
1.51-1.5770.13660051.297199.4
1.57-1.6370.12360061.438199.8
1.63-1.770.10959951.627199.5
1.7-1.7970.09159831.684199.5
1.79-1.970.06960181.577199.8
1.9-2.056.80.05559841.591199.4
2.05-2.267.60.04960601.8261100
2.26-2.597.70.04560422.0261100
2.59-3.267.70.03760542.0741100
3.26-507.40.0360901.863198.7

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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: 1.2→50 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.978 / SU B: 0.953 / SU ML: 0.02 / SU R Cruickshank DPI: 0.0343 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.032
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1329 6005 5 %RANDOM
Rwork0.1144 ---
obs0.1153 113625 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 70.37 Å2 / Biso mean: 14.018 Å2 / Biso min: 5.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.06 Å2
2---0.2 Å20 Å2
3---0.3 Å2
Refinement stepCycle: final / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 24 656 4252
Biso mean--19.18 29.32 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193897
X-RAY DIFFRACTIONr_bond_other_d0.0020.023555
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9415336
X-RAY DIFFRACTIONr_angle_other_deg0.93738280
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3825539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61824.713174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44615616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2731520
X-RAY DIFFRACTIONr_chiral_restr0.0850.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214494
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02774
X-RAY DIFFRACTIONr_rigid_bond_restr0.83837444
X-RAY DIFFRACTIONr_sphericity_free22.1975358
X-RAY DIFFRACTIONr_sphericity_bonded5.37357622
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.165 429 -
Rwork0.153 8234 -
all-8663 -
obs--97 %
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)
12.8695-1.0053-4.18037.93160.69887.35430.0970.25660.4756-0.25360.3798-0.1976-0.4077-0.1656-0.47680.0813-0.07-0.02610.11220.07420.1498-4.54932.891333.4849
21.58350.3835-0.39262.2125-0.26011.9831-0.03560.0916-0.0243-0.1963-0.0230.15260.01-0.11420.05850.03130.0007-0.02840.0284-0.01930.03989.718731.291131.6429
30.75330.0060.21691.10760.14090.74240.005-0.03330.04860.018-0.04820.08130.0188-0.02940.04320.0261-0.00860.00510.0219-0.00950.021317.025233.853942.0036
41.10830.1110.35324.0061-0.00020.785-0.00670.01390.1050.0105-0.0274-0.29090.05470.0710.03410.0346-0.003-0.00310.010.00370.032826.995327.741450.1087
50.89490.27750.18121.33150.36040.88320.0465-0.0267-0.04510.0604-0.03830.01260.0811-0.0256-0.00830.0435-0.0060.00010.00560.00310.013321.634818.177139.9686
67.56580.1606-2.36552.30770.11672.982-0.0062-0.0785-0.0941-0.1228-0.0346-0.20050.12290.29970.04080.0560.0098-0.00130.03820.00720.030925.857910.835631.2173
78.44160.0412-3.62160.09790.64796.18480.0588-0.05090.5014-0.02550.04080.0187-0.24250.2347-0.09960.02920.0122-0.00360.0503-0.00440.067728.645332.75915.7488
82.9515-1.5289-0.16453.06050.32542.1849-0.1051-0.18570.05690.25810.0293-0.0082-0.2141-0.08740.07580.0570.0045-0.02450.0271-0.0010.044411.72232.458717.5705
91.06870.1080.26521.17630.08980.8244-0.05750.06840.0648-0.0675-0.0115-0.1439-0.08430.09850.0690.0223-0.0118-0.00120.0140.01320.02839.719632.53556.3657
101.14320.2210.85982.4550.22531.3215-0.0316-0.01220.1316-0.122-0.04310.2744-0.0499-0.09780.07470.0357-0.0017-0.0160.0224-0.00260.0425-2.793625.5934-1.1354
110.7781-0.28340.27680.9401-0.17550.6718-0.0046-0.0069-0.0146-0.0049-0.014-0.00650.02520.01230.01860.0222-0.00540.00670.011-0.00330.01453.580516.227410.3355
127.70850.5546-0.3941.3231-0.60242.8386-0.0714-0.0815-0.25160.04520.08030.1032-0.0084-0.2529-0.00890.03330.00650.02190.02950.0140.0322-3.174810.048421.2887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 39
2X-RAY DIFFRACTION2A40 - 67
3X-RAY DIFFRACTION3A68 - 148
4X-RAY DIFFRACTION4A149 - 168
5X-RAY DIFFRACTION5A169 - 254
6X-RAY DIFFRACTION6A255 - 269
7X-RAY DIFFRACTION7B29 - 43
8X-RAY DIFFRACTION8B44 - 71
9X-RAY DIFFRACTION9B72 - 137
10X-RAY DIFFRACTION10B138 - 166
11X-RAY DIFFRACTION11B167 - 256
12X-RAY DIFFRACTION12B257 - 270

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