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- PDB-5zgr: Crystal structure of NDM-1 at pH7.3 (HEPES) in complex with hydro... -

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Basic information

Entry
Database: PDB / ID: 5zgr
TitleCrystal structure of NDM-1 at pH7.3 (HEPES) 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 / 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
Chem-ZZ7 / 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 / 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)52,3529
Polymers51,2642
Non-polymers1,0897
Water12,574698
1
A: 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 area10010 Å2
MethodPISA
2
B: Metallo-beta-lactamase type 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2225
Polymers25,6321
Non-polymers5904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area270 Å2
ΔGint-1 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.142, 79.215, 134.141
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
#3: 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
#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.: 698 / 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: 39.36 % / Mosaicity: 0.534 ° / Mosaicity esd: 0.004 °
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 0.1M HEPES pH7.3, 20% 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: 139092 / % possible obs: 93.4 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.074 / Χ2: 1.09 / Net I/σ(I): 8.4 / Num. measured all: 849054
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.15-1.196.30.514133870.807191
1.19-1.246.40.418133470.841190.8
1.24-1.36.40.334132020.903189.5
1.3-1.366.30.262131800.984189.3
1.36-1.456.10.2132841.034189.8
1.45-1.565.90.146136331.12192.1
1.56-1.725.70.114140131.253194.4
1.72-1.975.60.102145711.465197.4
1.97-2.485.70.07149581.253199.5
2.48-506.70.038155171.236199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0218refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
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: 0.981 / Cor.coef. Fo:Fc free: 0.975 / WRfactor Rfree: 0.1468 / WRfactor Rwork: 0.1288 / FOM work R set: 0.9189 / SU B: 0.935 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0338 / SU Rfree: 0.0323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1476 6951 5 %RANDOM
Rwork0.129 ---
obs0.13 132045 93.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 103.42 Å2 / Biso mean: 17.641 Å2 / Biso min: 9.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3598 0 60 698 4356
Biso mean--15.05 32.66 -
Num. residues----483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193836
X-RAY DIFFRACTIONr_bond_other_d0.0010.023459
X-RAY DIFFRACTIONr_angle_refined_deg1.311.9485234
X-RAY DIFFRACTIONr_angle_other_deg0.8043.0037991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.155506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53424.699166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.36215578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8591518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2584
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02750
X-RAY DIFFRACTIONr_rigid_bond_restr6.33737287
X-RAY DIFFRACTIONr_sphericity_free22.1055356
X-RAY DIFFRACTIONr_sphericity_bonded7.70857517
LS refinement shellResolution: 1.148→1.178 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.202 478 -
Rwork0.187 8960 -
all-9438 -
obs--86.56 %
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)
15.212-0.4841-0.87352.176-3.70286.89920.0662-0.1905-0.211-0.33860.00350.08180.6197-0.0125-0.06970.1503-0.0883-0.00980.1567-0.00730.0133-7.741-36.01630.418
28.476-1.7011-4.98752.27650.496111.35270.058-0.2448-0.09560.24630.09510.10420.4904-0.3893-0.15320.1227-0.046-0.02510.06190.02760.1324-12.595-40.83822.405
34.5287-0.69091.70860.9131-0.3322.807-0.033-0.0481-0.15930.06110.0260.06430.16550.02420.00690.0782-0.01670.00130.0272-0.00820.0569-9.626-34.24719.225
40.8972-0.15980.3070.88930.13781.1840.04030.092-0.1103-0.0572-0.01450.0480.1497-0.0404-0.02590.0743-0.0107-0.01160.0511-0.01820.0547-7.166-33.20512.22
50.6557-0.01350.04980.4285-0.00210.3808-0.00830.07660.003-0.02180.00240.01610.0303-0.03150.00580.0471-0.0055-0.00430.0599-0.00250.0439-7.651-18.04912.05
60.80470.05430.29540.95890.0570.5667-0.0026-0.0942-0.01440.1257-0.02140.02840.0299-0.03730.02390.0499-0.00460.01070.0682-0.00090.0427-14.853-16.61924.968
73.69823.13162.07524.26171.62572.08780.126-0.33090.1540.3145-0.23460.1441-0.1073-0.18460.10870.0796-0.00860.02490.0764-0.01830.0347-18.206-13.49830.674
87.7487-0.0412-0.08971.19182.0553.54760.17050.1430.2292-0.1969-0.071-0.06-0.357-0.1078-0.09950.1945-0.0428-0.03680.09080.02270.02695.75323.38227.106
97.29652.65590.39211.75690.49067.0479-0.121-0.0519-0.25870.17170.0996-0.2131-0.63310.38530.02140.1473-0.0102-0.01520.0407-0.02860.07483.02628.12518.076
102.7853-0.0491-1.97810.6993-0.01334.5473-0.0289-0.15410.09370.0960.0098-0.0341-0.03460.05240.01920.06610.0008-0.01340.04260.00240.06722.37921.01616.85
110.37550.0052-0.10470.6468-0.24151.5058-0.00040.00630.07680.03140.01160.0021-0.0882-0.0242-0.01130.05170.0029-0.00420.05030.00390.0621-3.86520.59411.54
120.4788-0.16460.00470.5418-0.09540.18320.00140.0357-0.0021-0.01290.00350.024-0.0078-0.0306-0.00480.0491-0.0012-0.00490.05910.00460.0547-5.4444.43911.021
130.51510.0838-0.08620.9191-0.21640.6533-0.0066-0.02150.02920.0713-0.0209-0.0709-0.01780.0290.02740.0459-0.0003-0.01110.06690.0060.06818.9825.50417.662
141.91271.8335-0.94383.4049-1.77513.15910.0827-0.181-0.08160.2194-0.2004-0.13420.12910.15110.11760.0493-0.0022-0.01510.06060.01890.061914.590.96922.95
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 38
2X-RAY DIFFRACTION2A39 - 46
3X-RAY DIFFRACTION3A47 - 68
4X-RAY DIFFRACTION4A69 - 112
5X-RAY DIFFRACTION5A113 - 213
6X-RAY DIFFRACTION6A214 - 254
7X-RAY DIFFRACTION7A255 - 270
8X-RAY DIFFRACTION8B30 - 39
9X-RAY DIFFRACTION9B40 - 49
10X-RAY DIFFRACTION10B50 - 68
11X-RAY DIFFRACTION11B69 - 115
12X-RAY DIFFRACTION12B116 - 197
13X-RAY DIFFRACTION13B198 - 254
14X-RAY DIFFRACTION14B255 - 270

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