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- PDB-6c89: NDM-1 Beta-Lactamase Exhibits Differential Active Site Sequence R... -

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Basic information

Entry
Database: PDB / ID: 6c89
TitleNDM-1 Beta-Lactamase Exhibits Differential Active Site Sequence Requirements for the Hydrolysis of Penicillin versus Carbapenem Antibiotics
ComponentsBeta-lactamase
KeywordsANTIMICROBIAL PROTEIN / NDM-1 / beta-lactamase / deep sequencing / antibiotic resistance / beta-lactams
Function / homology
Function and homology information


: / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75006148726 Å
AuthorsPalzkill, T. / Sun, Z. / Sankaran, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI106863 United States
CitationJournal: Nat Commun / Year: 2018
Title: Differential active site requirements for NDM-1 beta-lactamase hydrolysis of carbapenem versus penicillin and cephalosporin antibiotics.
Authors: Sun, Z. / Hu, L. / Sankaran, B. / Prasad, B.V.V. / Palzkill, T.
History
DepositionJan 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,75819
Polymers97,9024
Non-polymers85615
Water12,160675
1
A: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,09414
Polymers73,4263
Non-polymers66711
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6915
Polymers24,4751
Non-polymers2164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6655
Polymers24,4751
Non-polymers1894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6655
Polymers24,4751
Non-polymers1894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.167, 68.861, 68.441
Angle α, β, γ (deg.)92.230, 77.026, 91.840
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase / Beta-lactamase NDM-1 / BlaNDM-1 / BlaNDM-1 metallo beta lactamase / Class B beta-lactamase NDM-1 / ...Beta-lactamase NDM-1 / BlaNDM-1 / BlaNDM-1 metallo beta lactamase / Class B beta-lactamase NDM-1 / Metallo-beta-lactamase / Metallo-beta-lactamase NDM-1 / NDM-1 metallo-beta-lactamase / New Delhi metallo-beta-lactamase NDM-1 / Subclass B1 metallo-beta-lactamase NDM-1


Mass: 24475.492 Da / Num. of mol.: 4 / Mutation: K224R/G232A/N233Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: blaNDM-1, bla NDM-1, AM434_27040, APU18_05360, AZ95_0035, BET08_16280, BVL39_26630, CA268_28970, ECS01_0033, MS6198_A142, NDM1Dok01_N0175, pNDM102337_147, pNDM10505_149
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5KIY2

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Non-polymers , 6 types, 690 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 675 / 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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M LiCl, 0.1 M HEPES, pH7.0, 20% (w/v) PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→48.668 Å / Num. obs: 75377 / % possible obs: 91.07 % / Redundancy: 2.3 % / Biso Wilson estimate: 16.0102224723 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 17.6
Reflection shellResolution: 1.75→1.813 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.325 / Num. unique obs: 4529 / % possible all: 54.76

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Processing

Software
NameVersionClassification
phenix.refine1.12_2829refinement
PHENIX1.12_2829refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q6X

3q6x
PDB Unreleased entry


Resolution: 1.75006148726→37.2364552136 Å / SU ML: 0.172754826987 / Cross valid method: FREE R-VALUE / σ(F): 1.96361990839 / Phase error: 20.1253550062
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.19952021866 3746 4.97014727345 %
Rwork0.156087511804 71624 -
obs0.158241721583 75370 91.0727663791 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.4899005082 Å2
Refinement stepCycle: LAST / Resolution: 1.75006148726→37.2364552136 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6818 0 26 675 7519
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005460082928787015
X-RAY DIFFRACTIONf_angle_d0.7670765715859555
X-RAY DIFFRACTIONf_chiral_restr0.05311106217111068
X-RAY DIFFRACTIONf_plane_restr0.004675966681141267
X-RAY DIFFRACTIONf_dihedral_angle_d11.99812025444120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7501-1.77220.26109667932670.200392391951374X-RAY DIFFRACTION46.6192170819
1.7722-1.79550.243897252592870.1912149610751616X-RAY DIFFRACTION56.1305207647
1.7955-1.82010.251195974359970.1894025891111929X-RAY DIFFRACTION66.5571616294
1.8201-1.84610.2589844168151030.1791373765442308X-RAY DIFFRACTION78.0258899676
1.8461-1.87370.2219970714911340.1840768735242458X-RAY DIFFRACTION86.4
1.8737-1.9030.2281242114861360.1812871015792669X-RAY DIFFRACTION90.0770712909
1.903-1.93420.2247141628211370.1738079899442652X-RAY DIFFRACTION91.5026246719
1.9342-1.96750.2318518961651660.1723105770012731X-RAY DIFFRACTION94.0279130153
1.9675-2.00330.2214160580261670.1720824844222716X-RAY DIFFRACTION94.2156862745
2.0033-2.04180.2225037507851570.1613617875552780X-RAY DIFFRACTION95.233463035
2.0418-2.08350.2230598975121310.1607448055612808X-RAY DIFFRACTION96.1714659686
2.0835-2.12880.2301949211041440.1607320909072812X-RAY DIFFRACTION96.6328865642
2.1288-2.17830.1902802923431540.1574212473052789X-RAY DIFFRACTION96.1764705882
2.1783-2.23280.192772659791540.1517179682782790X-RAY DIFFRACTION96.4297412381
2.2328-2.29310.2101142115051460.1582710823512873X-RAY DIFFRACTION97.230273752
2.2931-2.36060.2247294479811440.1579678558192833X-RAY DIFFRACTION97.414921466
2.3606-2.43680.1937851481871490.1637702815392859X-RAY DIFFRACTION97.5673045735
2.4368-2.52380.2266619629811420.1659929142752837X-RAY DIFFRACTION97.3529411765
2.5238-2.62490.2519735709151290.1598116430352855X-RAY DIFFRACTION97.6439790576
2.6249-2.74430.1786835743291530.1610171306762862X-RAY DIFFRACTION98.2404692082
2.7443-2.88890.1965558845561310.1496550689892871X-RAY DIFFRACTION98.200850507
2.8889-3.06990.1983082813981550.160575259132865X-RAY DIFFRACTION98.2433311646
3.0699-3.30670.1976192213161630.1514105425672851X-RAY DIFFRACTION98.4645540673
3.3067-3.63930.1817670754531450.1421854393272886X-RAY DIFFRACTION98.7940026076
3.6393-4.16530.1618815850951690.1367715428512847X-RAY DIFFRACTION99.1127177128
4.1653-5.24550.1653590740631460.1320616858242899X-RAY DIFFRACTION98.6075129534
5.2455-37.24490.1967242512521400.1674213345292854X-RAY DIFFRACTION98.0032733224

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