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- PDB-3spu: apo NDM-1 Crystal Structure -

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Basic information

Entry
Database: PDB / ID: 3spu
Titleapo NDM-1 Crystal Structure
ComponentsBeta-lactamase NDM-1
KeywordsHYDROLASE / alpha beta/beta alpha sandwich / beta lactam antibiotics / periplasmic space
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
Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsStrynadka, N.C.J. / King, D.T.
CitationJournal: Protein Sci. / Year: 2011
Title: Crystal structure of New Delhi metallo-beta-lactamase reveals molecular basis for antibiotic resistance
Authors: King, D. / Strynadka, N.
History
DepositionJul 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2011Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Oct 30, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id
Revision 2.1Sep 13, 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 / struct_ncs_dom_lim / struct_site
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase NDM-1
B: Beta-lactamase NDM-1
C: Beta-lactamase NDM-1
D: Beta-lactamase NDM-1
E: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,81315
Polymers141,1595
Non-polymers65410
Water8,791488
1
A: Beta-lactamase NDM-1
C: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7256
Polymers56,4642
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase NDM-1
D: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7256
Polymers56,4642
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3633
Polymers28,2321
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.536, 73.904, 77.407
Angle α, β, γ (deg.)70.320, 75.860, 65.300
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
31B
41D
51E

NCS domain segments:

Ens-ID: 1 / Refine code: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGTHRTHRCC45 - 6219 - 36
21ARGARGTHRTHRAA45 - 6219 - 36
31ARGARGTHRTHRBB45 - 6219 - 36
41ARGARGTHRTHRDD45 - 6219 - 36
51ARGARGTHRTHREE45 - 6219 - 36
12GLYGLYLEULEUCC71 - 20945 - 183
22GLYGLYLEULEUAA71 - 20945 - 183
32GLYGLYLEULEUBB71 - 20945 - 183
42GLYGLYLEULEUDD71 - 20945 - 183
52GLYGLYLEULEUEE71 - 20945 - 183
13ASPASPASPASPCC225 - 267199 - 241
23ASPASPASPASPAA225 - 267199 - 241
33ASPASPASPASPBB225 - 267199 - 241
43ASPASPASPASPDD225 - 267199 - 241
53ASPASPASPASPEE225 - 267199 - 241

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Components

#1: Protein
Beta-lactamase NDM-1 / NDM-1 / Metallo-beta-lactamase NDM-1


Mass: 28231.799 Da / Num. of mol.: 5 / Fragment: unp residues 27-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pET41b / Production host: Escherichia coli (E. coli) / References: UniProt: C7C422, beta-lactamase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / 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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: .1M lithium sulfate, .63M ammonium sulfate, .05M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 27, 2011
RadiationMonochromator: Double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→49.21 Å / Num. all: 73129 / Num. obs: 70204 / % possible obs: 96 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.21 Å / % possible all: 89.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WHG

2whg


Resolution: 2.1→43.67 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 3563 5.1 %RANDOM
Rwork0.2161 ---
all0.242 73129 --
obs0.218 70203 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.9 Å2 / Biso mean: 28.4509 Å2 / Biso min: 9.37 Å2
Baniso -1Baniso -2Baniso -3
1-2.15 Å2-1.18 Å2-1.13 Å2
2---0.35 Å20.39 Å2
3----0.53 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8632 0 10 488 9130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0218835
X-RAY DIFFRACTIONr_bond_other_d00.025678
X-RAY DIFFRACTIONr_angle_refined_deg1.7371.9312035
X-RAY DIFFRACTIONr_angle_other_deg4.447313887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.44551155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44124.483377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.399151311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4171539
X-RAY DIFFRACTIONr_chiral_restr0.1360.21347
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02110115
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021748
X-RAY DIFFRACTIONr_mcbond_it0.9381.55746
X-RAY DIFFRACTIONr_mcbond_other01.52364
X-RAY DIFFRACTIONr_mcangle_it1.84229145
X-RAY DIFFRACTIONr_scbond_it2.85133089
X-RAY DIFFRACTIONr_scangle_it4.9244.52890
Refine LS restraints NCS

Ens-ID: 1 / Number: 2440 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1CTIGHT POSITIONAL0.220.05
2ATIGHT POSITIONAL0.220.05
3BTIGHT POSITIONAL0.230.05
4DTIGHT POSITIONAL0.290.05
5ETIGHT POSITIONAL0.250.05
1CTIGHT THERMAL0.230.5
2ATIGHT THERMAL0.290.5
3BTIGHT THERMAL0.210.5
4DTIGHT THERMAL0.230.5
5ETIGHT THERMAL0.380.5
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 242 -
Rwork0.301 4244 -
all-4486 -
obs--82.95 %

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