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- PDB-5zgp: Crystal structure of NDM-1 at pH6.2 (Bis-Tris) in complex with hy... -

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Basic information

Entry
Database: PDB / ID: 5zgp
TitleCrystal structure of NDM-1 at pH6.2 (Bis-Tris) 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
DI(HYDROXYETHYL)ETHER / Chem-ZZ7 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 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 / 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.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.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

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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)52,45810
Polymers51,2642
Non-polymers1,1958
Water11,926662
1
A: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3286
Polymers25,6321
Non-polymers6965
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area9950 Å2
MethodPISA
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1304
Polymers25,6321
Non-polymers4983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.240, 79.130, 134.442
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 670 molecules

#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-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 662 / 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: 2.04 Å3/Da / Density % sol: 39.58 % / Mosaicity: 0.311 ° / Mosaicity esd: 0.005 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.1M Bis-Tris pH6.2, 0.2M Li2SO4, 15% PEG 3350, 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: 1.15→50 Å / Num. obs: 139039 / % possible obs: 93.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.068 / Χ2: 1.222 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.15-1.192.80.45113301.042177
1.19-1.243.70.382129320.912188.3
1.24-1.35.10.323134930.924191.7
1.3-1.365.10.245135830.958192.3
1.36-1.4550.185138101.017193.6
1.45-1.564.90.135141811.131196.1
1.56-1.724.90.099145521.074198.2
1.72-1.9750.08148601.296199.5
1.97-2.485.30.084149652.308199.9
2.48-505.60.041153331.173198.9

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Processing

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

3q6x
PDB Unreleased entry


Resolution: 1.15→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.087 / SU ML: 0.022 / SU R Cruickshank DPI: 0.0346 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.034
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1574 6945 5 %RANDOM
Rwork0.1324 ---
obs0.1337 131984 93.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.79 Å2 / Biso mean: 19.532 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--0.71 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 67 662 4323
Biso mean--16.71 32.66 -
Num. residues----482
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193847
X-RAY DIFFRACTIONr_bond_other_d0.0020.023519
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9525243
X-RAY DIFFRACTIONr_angle_other_deg0.9423.0038128
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0965508
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19124.41161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27815595
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3841519
X-RAY DIFFRACTIONr_chiral_restr0.0880.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02754
X-RAY DIFFRACTIONr_rigid_bond_restr1.22737358
X-RAY DIFFRACTIONr_sphericity_free25.715344
X-RAY DIFFRACTIONr_sphericity_bonded12.35657566
LS refinement shellResolution: 1.151→1.181 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 356 -
Rwork0.215 7458 -
all-7814 -
obs--71.71 %
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)
118.114610.19133.73775.74281.741315.55590.6296-0.6758-0.8350.4187-0.4075-0.4737-2.51210.6626-0.2220.494-0.1656-0.01930.24350.14510.11656.97624.62425.644
23.899-0.2012-2.67711.52430.03046.23640.0851-0.22690.26610.1487-0.0024-0.0322-0.36360.0898-0.08280.0626-0.0078-0.02270.0173-0.00410.07821.74822.9217.148
30.8465-0.0695-0.09181.2428-0.66373.140.00820.03660.10250.05240.00460.0147-0.1835-0.0582-0.01290.0541-0.0023-0.00720.02770.00350.0822-3.73520.23611.591
40.7659-0.1338-0.01650.7543-0.12710.6498-0.00960.01710.00570.0073-0.0035-0.02190.00840.01230.01310.0585-0.0022-0.0030.02860.00670.07130.3954.94314.008
53.30882.783-2.81246.5592-5.11737.91310.0204-0.224-0.15430.1942-0.1772-0.17760.290.22630.15680.06070.0053-0.02070.04560.01620.083314.6330.98223.061
69.40952.44241.34473.6237-4.034811.17080.3366-0.1423-0.3759-0.1197-0.15270.34291.1675-0.6937-0.18390.2153-0.14960.02390.1629-0.1060.1528-10.242-36.90329.208
77.5034-0.30423.51141.9529-0.28264.68850.2088-0.1152-0.54090.096-0.00620.08960.428-0.0211-0.20250.1376-0.0124-0.0020.022-0.00660.1004-9.999-35.70518.825
81.445-0.01090.72511.48920.4573.11050.08640.1258-0.1541-0.0731-0.02670.02830.26370.0106-0.05970.1038-0.0001-0.01010.0284-0.0130.08-6.778-32.9712.453
91.102-0.0910.02790.95450.05290.7756-0.01470.0192-0.01450.0241-0.00310.06870.0444-0.05650.01790.0625-0.0052-0.00470.0293-0.0030.0697-10.517-17.59816.868
1012.3697-0.37191.8549.0919-1.98395.90050.0123-0.58790.40290.612-0.23230.0748-0.2062-0.09540.21990.16590.00020.02740.1072-0.03590.0455-15.193-9.23133.697
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 42
2X-RAY DIFFRACTION2A43 - 68
3X-RAY DIFFRACTION3A69 - 115
4X-RAY DIFFRACTION4A116 - 254
5X-RAY DIFFRACTION5A255 - 270
6X-RAY DIFFRACTION6B30 - 42
7X-RAY DIFFRACTION7B43 - 67
8X-RAY DIFFRACTION8B68 - 114
9X-RAY DIFFRACTION9B115 - 263
10X-RAY DIFFRACTION10B264 - 270

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