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- PDB-4uam: 1.8 Angstrom crystal structure of IMP-1 metallo-beta-lactamase wi... -

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Basic information

Entry
Database: PDB / ID: 4uam
Title1.8 Angstrom crystal structure of IMP-1 metallo-beta-lactamase with a mixed iron-zinc center in the active site
ComponentsIMP-1 metallo-beta-lactamase
KeywordsHYDROLASE / antibiotic resistance / binuclear metal center
Function / homologyRibonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / 4-Layer Sandwich / Alpha Beta / : / CITRATE ANION / :
Function and homology information
Biological speciesPseudomonas aeruginosa NCGM2.S1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsCarruthers, T.J. / Carr, P.D. / Jackson, C.J. / Otting, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Iron(III) Located in the Dinuclear Metallo-beta-Lactamase IMP-1 by Pseudocontact Shifts.
Authors: Carruthers, T.J. / Carr, P.D. / Loh, C.T. / Jackson, C.J. / Otting, G.
History
DepositionAug 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Dec 24, 2014Group: Database references
Revision 1.4Aug 23, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / diffrn_detector ...citation / diffrn_detector / diffrn_radiation_wavelength / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.6Sep 27, 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 / refine_hist / struct_conn / struct_conn_type / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_conn_type.id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMP-1 metallo-beta-lactamase
B: IMP-1 metallo-beta-lactamase
C: IMP-1 metallo-beta-lactamase
D: IMP-1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,82816
Polymers100,5874
Non-polymers1,24112
Water17,457969
1
A: IMP-1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4574
Polymers25,1471
Non-polymers3103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: IMP-1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4574
Polymers25,1471
Non-polymers3103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: IMP-1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4574
Polymers25,1471
Non-polymers3103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: IMP-1 metallo-beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4574
Polymers25,1471
Non-polymers3103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.990, 75.910, 82.360
Angle α, β, γ (deg.)83.450, 75.300, 74.010
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

#1: Protein
IMP-1 metallo-beta-lactamase


Mass: 25146.676 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 19-246
Source method: isolated from a genetically manipulated source
Details: A post-translational modification was present in the single crystal: Cys158 was partially oxidized in the absence of metal in the Zn2 site to CSD
Source: (gene. exp.) Pseudomonas aeruginosa NCGM2.S1 (bacteria)
Gene: bla IMP, NCGM2_1757 / Plasmid: pET47B(+)
Details (production host): Gene inserted with a stop codon so as not to append hexahis purification tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G4LPN7
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 969 / 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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: drop contained 1ul protein (25-30mg/ml in 20mm HEPES, 50mm NaCl, ph7.5) with 1uL microseed reservoir (0.2M sodium acetate, 0.2M sodium citrate, 26% PEGMME 2K). Protein solution was heat- ...Details: drop contained 1ul protein (25-30mg/ml in 20mm HEPES, 50mm NaCl, ph7.5) with 1uL microseed reservoir (0.2M sodium acetate, 0.2M sodium citrate, 26% PEGMME 2K). Protein solution was heat-treated at 310K for 3-5 days prior to filtration and crystallisation screening. microseeding was essential for diffraction quality crystal growth. crystal grew over 2 weeks

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX111.2835
SYNCHROTRONAustralian Synchrotron MX121.7311
Detector
TypeIDDetectorDate
ADSC QUANTUM 210r1CCDMar 14, 2013
ADSC QUANTUM 210r2CCDMar 16, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Silicon Double CrystalSINGLE WAVELENGTHMx-ray1
2Silicon Double CrystalSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.28351
21.73111
ReflectionNumber: 381451 / Rmerge(I) obs: 0.044 / Χ2: 1.11 / D res high: 1.8 Å / Num. obs: 191354 / % possible obs: 91.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
1.81.851390210.403
8.0544.927196110.019
5.698.05382010.02
4.655.69491510.018
4.034.65594010.018
3.64.03660410.021
3.293.6739510.023
3.043.29831510.027
2.853.04895510.035
2.682.85959010.044
2.552.68996110.05
2.432.551066510.061
2.322.431104810.07
2.232.321121210.082
2.152.231198210.096
2.082.151229010.117
2.012.081255710.139
1.952.011318010.187
1.91.951336510.256
1.851.91369710.333
ReflectionResolution: 1.8→44.93 Å / Num. all: 381468 / % possible obs: 94.81 % / Redundancy: 3.9 % / Biso Wilson estimate: 19.81 Å2 / Rmerge(I) obs: 0.05521 / Net I/σ(I): 18.08
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.853.90.7650.48062.92758315574139020.56992.26
1.85-1.90.8580.3332.462733614928136970.4791.8
1.9-1.950.8820.2563.252666914672133650.36291.1
1.95-2.010.9380.1874.342630814256131800.26492.5
2.01-2.080.9630.1395.782506813794125570.19791
2.08-2.150.9740.1176.722452213256122900.16692.7
2.15-2.230.9810.0967.992391312874119820.13693.1
2.23-2.320.9840.0829.512238312282112120.11691.3
2.32-2.430.9890.0710.692203611866110480.09993.1
2.43-2.550.990.06112.272127211374106650.08693.8
2.55-2.680.9940.0514.4198721069499610.0793.1
2.68-2.850.9950.04416.06191371027095900.06293.4
2.85-3.040.9960.03519.0917868955289550.0593.8
3.04-3.290.9980.02724.9416566900483150.03892.3
3.29-3.60.9980.02330.0414743814273950.03390.8
3.6-4.030.9980.02133.4713154739866040.02989.3
4.03-4.650.9980.01836.8211828656259400.02690.5
4.65-5.690.9980.01837.519794550849150.02589.2
5.69-8.050.9980.0236.877579427038200.02889.5
8.050.9980.01942.023820234219610.02783.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.83 Å28.7 Å
Translation3.83 Å28.7 Å

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX1.9_1692refinement
Cootmodel building
PHASERphasing
XSCALEdata scaling
XDSdata reduction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DOO

2doo


Resolution: 1.8→44.927 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 19.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.182 9681 5.06 %Random Selection
Rwork0.1615 181585 --
obs0.1625 191266 91.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 200.8 Å2 / Biso mean: 34.3635 Å2 / Biso min: 10.89 Å2
Refinement stepCycle: final / Resolution: 1.8→44.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6900 0 80 969 7949
Biso mean--36.66 39.08 -
Num. residues----880
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067164
X-RAY DIFFRACTIONf_angle_d0.9629740
X-RAY DIFFRACTIONf_chiral_restr0.0371072
X-RAY DIFFRACTIONf_plane_restr0.0051224
X-RAY DIFFRACTIONf_dihedral_angle_d11.5282588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82070.2743040.26355751605586
1.8207-1.84210.28723260.26286073639992
1.8421-1.86460.26833220.24995997631992
1.8646-1.88820.2643030.24696043634692
1.8882-1.9130.23923240.23986185650992
1.913-1.93920.27582950.23655898619391
1.9392-1.96690.23773560.2096022637892
1.9669-1.99630.22423500.19656116646692
1.9963-2.02750.2193010.19576017631892
2.0275-2.06070.22423120.18896165647792
2.0607-2.09630.20972960.18915933622990
2.0963-2.13440.20883510.17596067641893
2.1344-2.17540.21043290.16966256658593
2.1754-2.21980.19983330.16535986631993
2.2198-2.26810.21672700.17286077634790
2.2681-2.32090.17783290.16056049637893
2.3209-2.37890.19343430.15986251659493
2.3789-2.44320.19293140.1676112642693
2.4432-2.51510.19283090.15686238654794
2.5151-2.59630.17183040.15466132643694
2.5963-2.6890.19313780.15466084646293
2.689-2.79670.1843570.16046169652694
2.7967-2.9240.17543030.16366243654693
2.924-3.07810.18563150.15886121643694
3.0781-3.27090.16683510.156101645292
3.2709-3.52330.14523590.13855986634591
3.5233-3.87770.15293190.13725859617890
3.8777-4.43840.1423150.12456002631791
4.4384-5.59030.1282790.12345927620689
5.5903-44.94090.17233340.1535725605987
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)
13.5-1.5527-1.99735.95910.946.4058-0.20410.04110.2733-0.2313-0.1868-0.0387-0.13010.5550.06440.2097-0.048-0.07130.1780.05240.235142.396624.962662.7668
23.5411-0.17890.05652.5849-0.09222.4147-0.0931-0.21980.3270.2576-0.0407-0.1846-0.2120.23820.020.1965-0.0191-0.03780.14510.01110.179640.469120.711471.8416
33.8407-0.7537-0.51272.8801-0.65292.6662-0.0481-0.3913-0.40380.13650.06030.13920.1019-0.0354-0.00150.13870.02220.01310.11320.03520.15336.11918.594373.872
42.6329-0.25160.32811.5566-0.95171.4089-0.0551-0.10520.10450.13140.01440.0918-0.1664-0.0835-0.02310.15420.00560.00770.1105-0.02280.180226.887817.688167.3676
54.76660.98670.22343.92560.11942.7682-0.18370.33970.1888-0.33270.00690.4147-0.2563-0.23580.12910.1990.0321-0.04460.23120.05450.206621.744322.514756.585
66.7723-3.0441-3.43753.4691.29336.0235-0.16970.32830.3536-0.05320.3340.2375-0.2243-0.1065-0.21420.2483-0.0615-0.05010.28980.07310.208528.963851.294992.1055
73.58060.592-0.232.44930.44161.8289-0.12510.3333-0.1291-0.1680.09720.16860.1562-0.12740.00050.1815-0.0156-0.00290.23030.02710.127930.868243.016397.585
84.66071.0381-0.54123.71270.34711.9442-0.0076-0.4694-0.05340.1445-0.11370.02210.07090.10290.05440.15740.01590.00820.24010.05740.115735.162542.7599109.9919
92.7780.5053-0.30811.6498-0.40211.7158-0.06150.0646-0.0028-0.14040.0314-0.09510.0650.11530.02240.16340.00770.0060.26030.01230.141444.444547.8869100.0479
103.54310.11810.36792.89470.76744.3789-0.1260.2760.3416-0.28880.2194-0.2884-0.27730.33-0.05050.2038-0.02990.04260.29570.11460.261949.570957.947493.7625
116.44162.13142.07746.19570.96556.1099-0.2178-0.3627-0.216-0.01850.42440.25020.3665-0.04-0.17710.20310.06180.03680.26390.05090.128932.869736.374349.8751
123.3851-0.9239-0.28822.6871.06012.0397-0.0905-0.26580.23920.11410.07730.0551-0.1105-0.07420.02320.16380.009-0.01070.176-0.00560.138434.862944.906244.5174
135.5652-0.96280.19672.4037-0.54623.031-0.00070.40780.1633-0.1139-0.04920.089-0.06250.07260.00570.1528-0.0264-0.01390.17730.03010.122839.261645.372932.2665
143.0498-0.57670.22440.7696-0.5211.734-0.0578-0.1410.15710.07950.0518-0.087-0.09680.0487-0.02110.1535-0.0115-0.00510.2005-0.02830.121648.485840.087842.0897
154.5566-0.4995-1.16182.69120.66864.5687-0.224-0.2767-0.39670.22670.2047-0.17470.3140.308-0.00030.19220.0321-0.02950.23130.05830.216753.594929.942648.1329
163.64342.70582.68725.91772.77748.031-0.2323-0.2078-0.5160.2402-0.0257-0.09490.0470.36960.09030.26180.05250.07480.19760.09310.322317.423-10.403378.9369
173.01610.3302-0.5052.19250.44942.0975-0.17930.1516-0.4432-0.10590.0761-0.12550.25890.0939-0.02590.189-0.00850.02710.1223-0.00930.190915.4813-6.243569.8229
185.35320.7836-0.99832.3125-0.09453.1709-0.04050.14790.3611-0.09160.12970.0643-0.09710.0467-0.07590.1612-0.0208-0.01910.12090.04120.160911.15755.833567.7289
192.81220.1916-0.59161.3881-0.50951.596-0.08740.0626-0.2044-0.09950.03040.0370.1677-0.1555-0.04680.1689-0.0159-0.00320.1299-0.01560.22051.9308-3.199674.3075
204.5603-0.7452-0.28824.68910.17663.0902-0.2203-0.4518-0.3280.29590.06280.29720.215-0.24910.14370.2026-0.02460.04150.27920.08290.2433-3.195-7.843385.1731
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 28 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 85 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 108 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 172 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 222 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 3 through 28 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 29 through 85 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 86 through 108 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 109 through 172 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 173 through 222 )B0
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 28 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 29 through 85 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 86 through 108 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 109 through 172 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 173 through 222 )C0
16X-RAY DIFFRACTION16chain 'D' and (resid 3 through 28 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 29 through 85 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 86 through 108 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 109 through 172 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 173 through 222 )D0

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Yorodumi

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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