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- PDB-3sfp: Crystal Structure of the Mono-Zinc-boundform of New Delhi Metallo... -

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Basic information

Entry
Database: PDB / ID: 3sfp
TitleCrystal Structure of the Mono-Zinc-boundform of New Delhi Metallo-beta-Lactamase-1 from Klebsiella pneumoniae
ComponentsBeta-lactamase NDM-1
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta-beta-alpha sandwich / periplasmic / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI
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
CITRIC ACID / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Binkowski, T.A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: Plos One / Year: 2011
Title: Structure of Apo- and Monometalated Forms of NDM-1 A Highly Potent Carbapenem-Hydrolyzing Metallo-beta-Lactamase
Authors: Kim, Y. / Tesar, C. / Mire, J. / Jedrzejczak, R. / Binkowski, A. / Babnigg, G. / Sacchettini, J. / Joachimiak, A.
History
DepositionJun 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Sep 28, 2011Group: Database references
Revision 1.4Mar 28, 2012Group: Database references
Revision 1.5Sep 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_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_atom_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,40723
Polymers100,4014
Non-polymers2,00619
Water5,837324
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6426
Polymers25,1001
Non-polymers5425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6426
Polymers25,1001
Non-polymers5425
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6737
Polymers25,1001
Non-polymers5736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4504
Polymers25,1001
Non-polymers3503
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Beta-lactamase NDM-1
hetero molecules

D: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,09210
Polymers50,2002
Non-polymers8918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_545-x+1/2,y-1/2,-z+3/41
Buried area2750 Å2
ΔGint-101 kcal/mol
Surface area18340 Å2
MethodPISA
6
C: Beta-lactamase NDM-1
hetero molecules

B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,31513
Polymers50,2002
Non-polymers1,11511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_545-x+1/2,y-1/2,-z+3/41
Buried area3660 Å2
ΔGint-122 kcal/mol
Surface area18150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.944, 97.944, 187.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThere are four copies in the asymmetric unit.

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 25100.152 Da / Num. of mol.: 4 / Fragment: sequence database residues 39-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: blaNDM-1 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: C7C422, beta-lactamase

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Non-polymers , 6 types, 343 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.7 M Ammonium sulfate, 25.5 % (w/v) PEG 4000, 15 % (v/v) Glycerol, 10 mM zinc chloride, 10 mM citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.2825 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2825 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. all: 42642 / Num. obs: 42642 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 30.32 Å2 / Rsym value: 0.104 / Net I/σ(I): 6.3
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 2066 / Rsym value: 0.57 / % possible all: 98.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_761)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 3Q6X

3q6x
PDB Unreleased entry


Resolution: 2.27→46.406 Å / SU ML: 0.68 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2135 5.03 %random
Rwork0.181 ---
all0.183 42468 --
obs0.183 42468 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.352 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso mean: 32.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.2811 Å20 Å2-0 Å2
2--4.2811 Å20 Å2
3----8.5623 Å2
Refinement stepCycle: LAST / Resolution: 2.27→46.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6876 0 112 324 7312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117190
X-RAY DIFFRACTIONf_angle_d1.3319793
X-RAY DIFFRACTIONf_dihedral_angle_d16.3732504
X-RAY DIFFRACTIONf_chiral_restr0.111075
X-RAY DIFFRACTIONf_plane_restr0.0071296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2702-2.3230.28541590.23592585274498
2.323-2.38110.30081510.2282632278399
2.3811-2.44550.28111400.214526342774100
2.4455-2.51740.26771410.19482688282999
2.5174-2.59870.24061380.188526452783100
2.5987-2.69150.25361190.17542685280499
2.6915-2.79930.24511470.19022675282299
2.7993-2.92670.2561490.19012629277899
2.9267-3.08090.25411390.19762690282999
3.0809-3.27390.23021390.17832701284099
3.2739-3.52660.24791470.179227062853100
3.5266-3.88140.25471370.175727292866100
3.8814-4.44260.19841530.149327442897100
4.4426-5.59570.19751360.150327792915100
5.5957-46.41570.19441400.19192811295194
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)
10.78930.6342-2.46058.3339-3.18477.7603-0.1987-0.28890.02590.8470.1443-0.4207-0.22380.10950.06290.24290.0613-0.03510.2927-0.04720.123267.382429.204896.6601
21.6943-0.65170.46682.9991-0.00632.3716-0.1554-0.49430.05330.37410.22060.1444-0.1505-0.1883-0.05870.15510.06130.01610.2536-0.03280.172358.223331.482192.5923
31.2268-0.24531.01010.0517-0.60697.4943-0.0231-0.5224-0.19260.2848-0.09310.24351.0103-0.82710.10290.266-0.01080.0450.37770.00880.288647.383132.030683.3546
41.9877-0.9189-0.12271.82130.69112.1542-0.0490.0688-0.08040.1426-0.10410.12380.2629-0.16770.13930.1555-0.03720.00830.15790.01680.130160.209627.370274.5465
51.687-0.9989-0.16454.081-0.73882.2393-0.1651-0.19640.04920.12140.10660.0917-0.1415-0.19060.07190.13710.0038-0.00780.2026-0.03810.121158.046279.28994.9045
61.981-1.04150.29411.71940.31972.0176-0.03010.0683-0.03240.1159-0.0840.1290.1751-0.19870.11580.1653-0.0440.03490.17950.01650.140758.089576.543377.1259
73.0252-0.3137-1.86317.3424-2.54448.2908-0.1484-0.64530.13980.7611-0.009-0.54770.20240.34110.19650.24470.0515-0.07820.3392-0.06250.22519.167329.619898.5492
85.80032.8019-1.13115.5614-1.27233.01520.0025-0.2122-1.1480.00690.2156-0.06910.3026-0.4254-0.17510.19980.00730.00510.31710.11870.427810.199221.671593.2764
92.0735-0.0174-0.02693.00840.08361.744-0.0896-0.34520.09920.10060.1102-0.1025-0.17560.0554-0.02770.1708-0.032-0.01670.2553-0.04110.235611.301133.367990.7694
102.0680.24241.50014.41980.07322.9428-0.1137-0.76270.21420.79680.07450.0669-0.0574-0.3619-0.00660.22570.0597-0.00320.4-0.11630.24328.976736.982197.3593
111.83611.3209-0.3221.80440.68843.42240.0155-0.3056-0.3044-0.2629-0.42020.38420.1867-1.12680.32880.2947-0.0298-0.02960.4846-0.05330.24941.21732.028988.7941
124.7613-0.4222-0.87151.86921.74224.59720.1708-0.1130.49870.123-0.11820.1917-0.1495-0.68690.00060.1880.0665-0.03050.2699-0.04640.19350.829935.51377.8665
132.3274-0.78020.38772.6980.32052.61770.1387-0.0221-0.03660.1407-0.24830.04930.1442-0.14460.10970.1762-0.0056-0.00510.25380.01760.205111.533128.373577.0611
141.5483-0.57090.7622.4883-0.65065.13460.16060.0681-0.0860.2944-0.25480.10650.04630.35570.16320.22550.03270.05390.22780.01070.165318.652626.116877.3979
154.80910.8741-0.13719.53281.3687.61110.07980.661-0.1825-0.7083-0.17870.01830.7394-0.15120.14220.27830.02620.0430.3116-0.00560.181117.680517.113171.2208
160.94230.1274-1.26274.2251-1.71954.1220.036-0.43040.0250.4032-0.2386-0.4353-0.11640.61990.09390.16850.0322-0.08260.2765-0.02620.264419.503977.6344101.162
173.53140.85820.33143.8418-0.66052.57590.0099-0.1665-0.1318-0.17-0.05720.1133-0.0129-0.02860.07190.15090.00630.01120.1961-0.02790.169110.463176.667994.23
182.4124-0.55160.25411.5507-0.49514.1275-0.1239-0.1360.0597-0.0637-0.06520.2888-0.2766-0.67970.190.16640.0406-0.01250.2097-0.04210.22475.329182.925596.4122
194.5628-0.3524-1.05091.39090.97044.88910.00350.07850.0465-0.0171-0.16070.0546-0.0617-0.43370.15220.18910.0661-0.04440.2516-0.00710.16460.417384.153380.5764
201.3693-1.1570.52792.51650.62843.28240.17670.1696-0.0739-0.1096-0.29170.05750.1192-0.18830.09370.16360.01130.00050.27510.01740.172911.117977.011379.4957
211.3759-1.35160.88221.9711-0.20894.73720.07450.1199-0.07640.1907-0.29440.02190.10840.39760.29950.2380.020.0110.28190.01350.148118.269274.821479.7168
226.78712.1921-0.04572.0141.47847.51940.14190.6129-0.2536-0.59190.06510.08940.67130.0405-0.25240.30110.0834-0.03970.25850.00050.200817.545865.829673.0084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 40:57)
2X-RAY DIFFRACTION2chain 'A' and (resseq 58:118)
3X-RAY DIFFRACTION3chain 'A' and (resseq 119:152)
4X-RAY DIFFRACTION4chain 'A' and (resseq 153:270)
5X-RAY DIFFRACTION5chain 'B' and (resseq 40:137)
6X-RAY DIFFRACTION6chain 'B' and (resseq 138:270)
7X-RAY DIFFRACTION7chain 'C' and (resseq 40:57)
8X-RAY DIFFRACTION8chain 'C' and (resseq 58:71)
9X-RAY DIFFRACTION9chain 'C' and (resseq 72:94)
10X-RAY DIFFRACTION10chain 'C' and (resseq 95:118)
11X-RAY DIFFRACTION11chain 'C' and (resseq 119:137)
12X-RAY DIFFRACTION12chain 'C' and (resseq 138:170)
13X-RAY DIFFRACTION13chain 'C' and (resseq 171:228)
14X-RAY DIFFRACTION14chain 'C' and (resseq 229:255)
15X-RAY DIFFRACTION15chain 'C' and (resseq 256:270)
16X-RAY DIFFRACTION16chain 'D' and (resseq 39:57)
17X-RAY DIFFRACTION17chain 'D' and (resseq 58:94)
18X-RAY DIFFRACTION18chain 'D' and (resseq 95:137)
19X-RAY DIFFRACTION19chain 'D' and (resseq 138:170)
20X-RAY DIFFRACTION20chain 'D' and (resseq 171:228)
21X-RAY DIFFRACTION21chain 'D' and (resseq 229:255)
22X-RAY DIFFRACTION22chain 'D' and (resseq 256:270)

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