[English] 日本語
Yorodumi
- PDB-4hl1: Crystal Structure of New Delhi Metallo-beta-Lactamase-1, Complexe... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hl1
TitleCrystal Structure of New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Ampicillin
ComponentsBeta-lactamase NDM-1
KeywordsHydrolase/Antibiotic / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors / MTBI / alpha-beta-beta-alpha sandwich / hydrolase / Hydrolase-Antibiotic complex
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 / 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
: / Chem-ZZ7 / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Mire, J. / Sacchettini, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) / Structures of Mtb Proteins Conferring Susceptibility to Known Mtb Inhibitors (MTBI)
CitationJournal: To be Published
Title: Crystal Structure of New Delhi Metallo-beta-Lactamase-1, Complexed with Cd and Ampicillin
Authors: Kim, Y. / Tesar, C. / Jedrzejczak, R. / Babnigg, J. / Mire, J. / Sacchettini, J. / Joachimiak, A.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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_alt_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,91612
Polymers51,4362
Non-polymers1,48010
Water8,449469
1
A: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4586
Polymers25,7181
Non-polymers7405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase NDM-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4586
Polymers25,7181
Non-polymers7405
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-86 kcal/mol
Surface area18160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.997, 78.700, 134.377
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTwo monomers in the asymmetric unit

-
Components

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


Mass: 25717.914 Da / Num. of mol.: 2
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
#2: Chemical ChemComp-ZZ7 / (2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 367.420 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21N3O5S
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: B11: 0.2 M lithium sulfate, 0.1 M Bis-TrisHCl pH 6.5, 25 %(w/v) PEG 3350, 5 mM CdCl2, 100mM ampicillin, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2011 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 123712 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 13 Å2 / Rsym value: 0.096 / Net I/σ(I): 9.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 3509 / Rsym value: 0.782 / % possible all: 93.5

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.8.1_1161)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3q6X

3q6x
PDB Unreleased entry


Resolution: 1.5→34.942 Å / SU ML: 0.1 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.25 / Stereochemistry target values: ML
Details: BOTH F+ AND F- REFLECTIONS ARE USED TO BETTER REFINE CD IONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.149 6300 5.09 %random
Rwork0.137 ---
all0.137 123712 --
obs0.137 123712 96.72 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.9 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3557 0 52 469 4078
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113961
X-RAY DIFFRACTIONf_angle_d1.5815437
X-RAY DIFFRACTIONf_dihedral_angle_d14.2681429
X-RAY DIFFRACTIONf_chiral_restr0.097593
X-RAY DIFFRACTIONf_plane_restr0.007744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.5-1.51710.2552250.23553344356984
1.5171-1.53490.22772080.2213606381490
1.5349-1.55370.20671950.19753725392091
1.5537-1.57330.19011840.18443777396193
1.5733-1.5940.1991540.1733867402196
1.594-1.61590.18922000.1653857405794
1.6159-1.63890.14572150.15413821403695
1.6389-1.66340.17022370.14993892412997
1.6634-1.68940.19421950.14833906410195
1.6894-1.71710.14491810.14663829401096
1.7171-1.74670.19421950.1433947414297
1.7467-1.77850.16662330.13283897413096
1.7785-1.81270.16061860.1293950413698
1.8127-1.84970.14212340.12743953418797
1.8497-1.88990.13522080.13393941414998
1.8899-1.93380.14832070.1353957416497
1.9338-1.98220.14432290.12943977420699
1.9822-2.03580.14042020.12294004420699
2.0358-2.09570.14491980.12943992419099
2.0957-2.16330.14292260.1224036426299
2.1633-2.24060.11182820.12173912419499
2.2406-2.33030.12932280.12573995422399
2.3303-2.43630.13112100.130640624272100
2.4363-2.56480.16262180.1344010422899
2.5648-2.72540.14052050.13684030423599
2.7254-2.93570.17232080.138940364244100
2.9357-3.2310.13662110.136540534264100
3.231-3.6980.15732320.12493989422199
3.698-4.65740.12841960.119740424238100
4.6574-34.95190.1431980.14754005420398
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)
10.6419-0.41360.35121.2064-0.51884.54420.087-0.4482-0.23550.2659-0.03140.11810.4059-0.3351-0.00980.1735-0.04120.01740.21870.0260.1179-3.1504-23.023420.2626
21.4378-0.03620.37311.55090.56133.81380.02530.0097-0.15310.01850.0026-0.03660.13990.0296-0.01590.07110.00080.01020.0637-0.00310.06894.4144-19.835710.6843
31.2972-0.3447-0.04720.85850.22630.71970.0008-0.0046-0.04530.0049-0.01370.01020.0336-0.01760.0160.07940.00040.00970.0839-0.00560.05633.45-5.184212.4079
41.41610.16190.03741.723-0.02290.80580.0501-0.12410.0390.1417-0.07320.1795-0.03-0.06390.02060.0732-0.00050.03140.1106-0.01750.0894-10.5596-3.103320.368
54.121-0.2366-2.42861.5774-0.75294.14660.1519-0.73810.57420.35620.0039-0.0965-0.55560.2112-0.15830.277-0.0459-00.2497-0.07090.209412.645837.104321.4093
64.7108-0.5393-4.63832.6271-0.12687.1240.07-0.08590.04840.2796-0.05990.2505-0.1492-0.6163-0.02740.1634-0.00470.01080.2417-0.03090.08134.781532.371123.4702
71.82150.3072-0.2181.7663-0.30712.2771-0.00990.05940.1277-0.1141-0.02560.0701-0.2271-0.05760.02940.13630.02130.00140.10180.00370.06445.853730.003810.966
81.462-0.01890.22370.66630.0560.7787-0.01260.00730.02630.0002-0.0003-0.0264-0.02360.07110.01180.10020.00030.01290.10660.00130.064311.577816.299116.7274
95.47732.9706-2.64946.3743-3.16656.28890.024-0.5111-0.39430.4015-0.1622-0.17690.18640.19070.07250.1450.0258-0.01740.1650.01060.079118.327313.251731.3412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 70 )
2X-RAY DIFFRACTION2chain 'A' and (resid 71 through 118 )
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 215 )
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 269 )
5X-RAY DIFFRACTION5chain 'B' and (resid 31 through 57 )
6X-RAY DIFFRACTION6chain 'B' and (resid 58 through 70 )
7X-RAY DIFFRACTION7chain 'B' and (resid 71 through 137 )
8X-RAY DIFFRACTION8chain 'B' and (resid 138 through 255 )
9X-RAY DIFFRACTION9chain 'B' and (resid 256 through 270 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • 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

Read more