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- PDB-8i8f: Crystal structure of NDM-1 at pH5.5 (Succinate) in complex with h... -

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Basic information

Entry
Database: PDB / ID: 8i8f
TitleCrystal structure of NDM-1 at pH5.5 (Succinate) in complex with hydrolyzed compound 1
ComponentsMetallo beta lactamase NDM-1
KeywordsHYDROLASE-INHIBITOR / penicillin / hydrolase-inhibitor complex
Function / homology: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / beta-lactamase activity / metal ion binding / : / NDM-1
Function and homology information
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsShi, X. / Liu, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Interplay between the beta-lactam side chain and an active-site mobile loop of NDM-1 in penicillin hydrolysis as a potential target for mechanism-based inhibitor design.
Authors: Shi, X. / Dai, Y. / Lan, Z. / Wang, S. / Cui, L. / Xiao, C. / Zhao, K. / Li, X. / Liu, W. / Zhang, Q.
History
DepositionFeb 4, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallo beta lactamase NDM-1
B: Metallo beta lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1538
Polymers57,0552
Non-polymers1,0996
Water10,052558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.114, 78.847, 133.534
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Metallo beta lactamase NDM-1 / Metallo beta-lactamase / Metallo-beta-lactamase NDM1 / Metallobetalactamase NDM-1 / NDM-1 / NDM1 ...Metallo beta-lactamase / Metallo-beta-lactamase NDM1 / Metallobetalactamase NDM-1 / NDM-1 / NDM1 metallo-beta-lactamase / New Delhi Metallo carbapenemase-1 / New Delhi metallo-beta-lactamase NDM-1 / New Delhi metallo-beta-lactamse 1


Mass: 28527.428 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1, bla NDM-1, blaNDM1, NDM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: E9NWK5
#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-OL6 / (2R,4S)-5,5-dimethyl-2-[(1R)-1-(2-naphthalen-1-yloxyethanoylamino)-2-oxidanyl-2-oxidanylidene-ethyl]-1,3-thiazolidine-4-carboxylic acid


Mass: 418.463 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N2O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 558 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.8 Å3/Da / Density % sol: 31.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M Succinate pH5.5, 32%PEG3350 / PH range: 5.0-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.89→27.77 Å / Num. obs: 33742 / % possible obs: 98.86 % / Redundancy: 12.5 % / Biso Wilson estimate: 18.47 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.121 / Net I/σ(I): 22.92
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 2305 / CC1/2: 0.937

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
Cootmodel building
PHENIX1.19.1_4122phasing
PHENIX1.19.1_4122refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→27.77 Å / SU ML: 0.1529 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.41
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1895 1738 5.15 %
Rwork0.151 32004 -
obs0.1529 33742 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.79 Å2
Refinement stepCycle: LAST / Resolution: 1.89→27.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 62 558 4188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733761
X-RAY DIFFRACTIONf_angle_d0.94555140
X-RAY DIFFRACTIONf_chiral_restr0.0593571
X-RAY DIFFRACTIONf_plane_restr0.0065708
X-RAY DIFFRACTIONf_dihedral_angle_d6.3308568
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.940.28791110.1982305X-RAY DIFFRACTION86.84
1.94-20.19861400.16892654X-RAY DIFFRACTION99.93
2-2.080.21681540.15862664X-RAY DIFFRACTION100
2.08-2.160.18891560.16362642X-RAY DIFFRACTION99.96
2.16-2.260.2381450.15932652X-RAY DIFFRACTION99.89
2.26-2.380.23781580.15892652X-RAY DIFFRACTION100
2.38-2.530.21061400.16532679X-RAY DIFFRACTION99.89
2.53-2.720.19621330.16252697X-RAY DIFFRACTION99.68
2.72-2.990.21071460.1612696X-RAY DIFFRACTION99.93
2.99-3.430.17581640.14152692X-RAY DIFFRACTION99.9
3.43-4.310.14891410.12782782X-RAY DIFFRACTION100
4.32-27.770.15861500.14092889X-RAY DIFFRACTION99.97
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)
10.1245192643930.00986193920304-0.03231702593420.154682579202-0.02813370533050.09356697249180.1201346874180.394087116275-0.101290289481-0.39035829131-0.1103442990230.1995999539570.3961035054470.122163401151-0.00511055189950.3145115564610.0557567356412-0.0489011914160.2359375301380.02331508903640.233298268824-7.43929927242.06852049484-22.1401013391
20.2382669732060.10600086835-0.1487886926950.195349732718-0.2013742156740.242895949784-0.1843199822640.244174561813-0.117741488381-0.288679573516-0.1476690696240.2169073208770.162925007449-0.198525304063-0.2635947316190.217827631766-0.00921848952509-0.07690307943450.20789525061-0.0556351567520.191726507378-14.36977609346.86311035036-23.1604303829
30.523753658143-0.001501923195270.102302041170.994604959017-0.05167619791560.5079186469490.02961823743850.00193063944943-0.009729940711410.000359168932141-0.02182906722890.005008453728210.0356358804990.0188388392787-4.18833503772E-60.0942040997389-0.00482492771038-0.01369533157160.10244154320.01557560261850.0735376420794-10.021684648618.0898571965-14.850661295
40.01702215736380.01558569067690.01613525933370.05137459995090.01164359878440.02673858627020.05635989175150.3395030748310.278925958347-0.277531028312-0.163204864093-0.142703044154-0.3659760816950.134599040591-0.001561434618650.2302737231490.004611359661440.0139161577390.2317012627470.04212259205130.151526625028-1.2937286147426.175666841-31.1467660555
50.1648814655520.0639522087512-0.03836940939860.177665060154-0.09469587558510.594027181887-0.135263302277-0.3691812353740.02509944476530.422052337311-0.172176057458-0.149202049863-0.2058482504770.362093403819-0.02428201431920.319244242815-0.0487154305721-0.02017935100780.268992306032-0.006150260760680.217783946276-14.461406774324.6018168429-48.3412392919
60.680936462183-0.08278856005620.2075351816440.186351415725-0.0355946650550.06500480005240.0694702070986-0.5638114415410.2866399603110.21646149606-0.2591663372050.0902790840471-0.123358846015-0.184644670383-0.1377965075880.199289585016-0.05766945957310.009385335556740.270532671896-0.07992445953980.165135225782-20.189569901619.5379153943-43.824977258
70.4550298681680.115452597995-0.03820353467460.142769055542-0.1422668542670.1395850408510.04338973526390.01118514807770.269513570178-0.01245812607880.01068439672120.0450426995506-0.11217477172-0.03953720719750.02962538620410.1244020201020.02352897254870.009992979364980.09464109037980.01071954298280.147090245893-23.887398420219.7236237107-56.1605112418
80.3396267117670.0115984529697-0.1084481352320.7339395790320.0008371802023350.288156845390.01664875912850.003077677083490.06848183926910.0387477989857-0.00928077247709-0.11324543179-0.007698511182560.00885192156746-2.03757118779E-50.0930174135680.01023977819-0.01317532620320.09689818760480.0007263571713580.109443698974-19.22131450984.78695550377-52.6019104039
90.03754311761410.126596633738-0.02916328730960.6473875986520.05113306004980.104427068250.0316148123203-0.163319178737-0.007901600177570.403982207642-0.014196660742-0.2029402348780.2237373556110.101598686035-0.01285670120470.1695532348730.00456833250149-0.04564198946110.1994426261380.03317317093410.231667540221-5.313228194710.254777069078-43.2076363864
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 31 through 57 )AA31 - 571 - 27
22chain 'A' and (resid 58 through 70 )AA58 - 7028 - 40
33chain 'A' and (resid 71 through 255 )AA71 - 25541 - 225
44chain 'A' and (resid 256 through 270 )AA256 - 270226 - 240
55chain 'B' and (resid 32 through 57 )BE32 - 571 - 26
66chain 'B' and (resid 58 through 70 )BE58 - 7027 - 39
77chain 'B' and (resid 71 through 118 )BE71 - 11840 - 87
88chain 'B' and (resid 119 through 255 )BE119 - 25588 - 224
99chain 'B' and (resid 256 through 270 )BE256 - 270225 - 239

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