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- PDB-5zgv: Crystal structure of NDM-1 at pH8.0 (Tris) with 2 molecules per a... -

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Basic information

Entry
Database: PDB / ID: 5zgv
TitleCrystal structure of NDM-1 at pH8.0 (Tris) 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 / 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
HYDROXIDE ION / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.15 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)51,6519
Polymers51,2642
Non-polymers3887
Water11,548641
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7804
Polymers25,6321
Non-polymers1483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-58 kcal/mol
Surface area10620 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-61 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.678, 73.716, 66.605
Angle α, β, γ (deg.)90.000, 98.400, 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 1.93 Å3/Da / Density % sol: 36.17 % / Mosaicity: 0.525 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1M Tris pH8.0, 25% PEG 3350

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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: 1.15→50 Å / Num. obs: 136383 / % possible obs: 99 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.072 / Χ2: 1.224 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.15-1.193.40.497136260.938199.1
1.19-1.243.40.375135880.947199
1.24-1.33.50.292136160.962199
1.3-1.363.50.216135810.986198.9
1.36-1.453.50.17136301.102199
1.45-1.563.60.135136031.297199.1
1.56-1.723.60.111137351.391199.6
1.72-1.973.60.076137501.375199.7
1.97-2.483.70.062137161.579199.4
2.48-503.60.048135381.568196.8

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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: 1.15→50 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.026 / SU ML: 0.021 / SU R Cruickshank DPI: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.031
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1438 6848 5 %RANDOM
Rwork0.1232 ---
obs0.1242 129503 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 93.12 Å2 / Biso mean: 16.286 Å2 / Biso min: 7.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å2-0.08 Å2
2---0.4 Å20 Å2
3---0.56 Å2
Refinement stepCycle: final / Resolution: 1.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 12 641 4225
Biso mean--13.94 30.93 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193881
X-RAY DIFFRACTIONr_bond_other_d0.0020.023547
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.945318
X-RAY DIFFRACTIONr_angle_other_deg0.93538263
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75724.767172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.58215617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8271519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214478
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02769
X-RAY DIFFRACTIONr_rigid_bond_restr0.85737420
X-RAY DIFFRACTIONr_sphericity_free23.1055373
X-RAY DIFFRACTIONr_sphericity_bonded5.13757566
LS refinement shellResolution: 1.148→1.178 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 495 -
Rwork0.215 9155 -
all-9650 -
obs--94.74 %
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)
12.6760.0066-4.77235.9581.95189.1580.14180.14150.3872-0.61370.52450.0729-0.4567-0.0791-0.66620.0712-0.0480.00590.06150.06640.259-4.655232.89933.4737
21.52040.2976-0.34692.141-0.15751.9011-0.04050.0864-0.0292-0.2146-0.02440.1390.0001-0.12320.06490.0415-0.0001-0.03460.0392-0.01780.03999.62831.318731.6573
30.7031-0.01090.20880.950.15670.7178-0.0111-0.0280.0528-0.019-0.0310.0860.0063-0.04840.04210.0254-0.0059-0.00410.0268-0.00740.024816.057433.993541.6785
41.1159-0.07630.20852.99670.29231.17370.00530.01950.14270.02660.0245-0.25110.03520.173-0.02990.02380.0021-0.00750.0337-0.00350.039828.404729.379750.1207
50.91910.21810.09571.27950.42180.97370.041-0.0234-0.01970.07-0.0181-0.00750.0922-0.0204-0.02280.0476-0.0047-0.00550.01060.00270.01622.521718.048541.3053
61.3858-0.1121-0.05912.21340.11441.54890.0061-0.0003-0.1143-0.0663-0.0205-0.04060.07590.05330.01440.0507-0.0047-0.01020.0211-0.00530.017821.064514.171532.5463
73.7115-0.6725-0.12920.38560.51140.9235-0.0239-0.12870.2345-0.03420.0565-0.0658-0.07630.088-0.03260.0227-0.0113-0.01810.03760.01290.059220.775531.494715.7714
829.2897-8.8052-24.42212.503710.132721.15981.3513-0.3060.37371.1161-1.2280.6167-0.7193-0.1721-0.12340.3843-0.02130.19690.62530.05040.1105-1.458236.9523.5519
90.99130.03660.28481.02970.01790.9484-0.05450.0710.0765-0.0325-0.0232-0.125-0.11260.12460.07770.0328-0.0161-0.01230.02110.01660.02779.693432.56676.3985
101.3934-0.11270.66822.0131-0.17022.593-0.0286-0.01280.1871-0.0533-0.02430.2728-0.0807-0.14060.05280.0339-0.0005-0.01680.0226-0.00260.0678-3.249827.898-1.0741
110.7291-0.27960.36010.8912-0.23980.7720.0081-0.0078-0.0226-0.0104-0.01210.00240.02550.01280.0040.0344-0.0045-0.00140.021-0.00060.02363.371316.02899.9443
128.4180.6154-0.34631.3236-0.45313.2571-0.0405-0.0958-0.26810.0470.05960.12340.0172-0.3128-0.01910.04210.00450.01590.04280.02040.038-3.407710.187921.0731
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 39
2X-RAY DIFFRACTION2A40 - 67
3X-RAY DIFFRACTION3A68 - 145
4X-RAY DIFFRACTION4A146 - 167
5X-RAY DIFFRACTION5A168 - 241
6X-RAY DIFFRACTION6A242 - 269
7X-RAY DIFFRACTION7B29 - 63
8X-RAY DIFFRACTION8B64 - 71
9X-RAY DIFFRACTION9B72 - 137
10X-RAY DIFFRACTION10B138 - 162
11X-RAY DIFFRACTION11B163 - 256
12X-RAY DIFFRACTION12B257 - 270

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