[English] 日本語
Yorodumi
- PDB-6ao1: Crystal structure of a beta-lactamase from Burkholderia phymatum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ao1
TitleCrystal structure of a beta-lactamase from Burkholderia phymatum
ComponentsBeta-lactamase domain protein
KeywordsHYDROLASE / NIAID / structural genomics / beta-lactamase / metalloenzyme / calcium / zinc / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase-like, C-terminal domain / : / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Beta-lactamase domain protein
Similarity search - Component
Biological speciesParaburkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a beta-lactamase from Burkholderia phymatum
Authors: Edwards, T.E. / Delker, S.L. / Lorimer, D.D.
History
DepositionAug 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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_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.ptnr1_symmetry / _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.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)162,75228
Polymers161,6364
Non-polymers1,11624
Water21,4021188
1
A: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6536
Polymers40,4091
Non-polymers2445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,81410
Polymers40,4091
Non-polymers4059
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6727
Polymers40,4091
Non-polymers2626
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6135
Polymers40,4091
Non-polymers2044
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.300, 70.800, 82.580
Angle α, β, γ (deg.)90.470, 98.620, 112.460
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Beta-lactamase domain protein


Mass: 40409.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum (bacteria) / Gene: Bphy_0182 / Production host: Escherichia coli (E. coli) / References: UniProt: B2JKI6
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1188 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18.6 mg/mL BuphA.15997.PS38000 against MCSG screen condition C7 (200 mM calcium chloride, 0.1 M Tris, pH 8.5, 20% PEG4000), cryoprotectant: 15% ethylene glycol, crystal tracking ID 290667h5, ...Details: 18.6 mg/mL BuphA.15997.PS38000 against MCSG screen condition C7 (200 mM calcium chloride, 0.1 M Tris, pH 8.5, 20% PEG4000), cryoprotectant: 15% ethylene glycol, crystal tracking ID 290667h5, unique puck ID cho2-5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.8→35.057 Å / Num. obs: 128398 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 2.926 % / Biso Wilson estimate: 23.49 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.053 / Χ2: 1.025 / Net I/σ(I): 14.85 / Num. measured all: 375743 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.852.5390.3532.7294380.870.44195.7
1.85-1.92.8450.2753.7891660.9280.3495.9
1.9-1.952.990.2224.989370.9520.27396.3
1.95-2.012.990.1646.3786850.9720.20296.3
2.01-2.082.9880.1327.7884800.9820.16296.5
2.08-2.152.9850.1039.782100.9880.12796.6
2.15-2.232.9870.08511.4979270.9910.10596.7
2.23-2.322.9790.07413.0575710.9920.09296.9
2.32-2.432.9790.06214.8973510.9950.07797
2.43-2.552.9710.05516.8769640.9950.06897.1
2.55-2.682.970.04818.7266830.9960.0697.2
2.68-2.852.9680.04221.2663010.9960.05297
2.85-3.042.9560.03823.7559070.9960.04797.2
3.04-3.292.9370.03526.155330.9970.04397.7
3.29-3.62.9360.03128.5450870.9970.03997.5
3.6-4.022.9280.0329.8346070.9970.03797.4
4.02-4.652.9360.02931.0640520.9970.03697.7
4.65-5.692.9350.0283134380.9970.03598.1
5.69-8.052.8970.02930.8226600.9970.03598
8.05-35.0572.8280.02931.6914010.9970.03694

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5U8O

5u8o


Resolution: 1.8→35.057 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 21.93
RfactorNum. reflection% reflection
Rfree0.2006 1980 1.54 %
Rwork0.1636 --
obs0.1641 128371 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.8 Å2 / Biso mean: 34.3218 Å2 / Biso min: 11.79 Å2
Refinement stepCycle: final / Resolution: 1.8→35.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10847 0 45 1199 12091
Biso mean--39.45 39.25 -
Num. residues----1412
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611269
X-RAY DIFFRACTIONf_angle_d0.81415351
X-RAY DIFFRACTIONf_chiral_restr0.0571685
X-RAY DIFFRACTIONf_plane_restr0.0052008
X-RAY DIFFRACTIONf_dihedral_angle_d14.6976630
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8450.27931430.2278933907696
1.845-1.89480.2761430.21158948909196
1.8948-1.95060.22841230.20559017914096
1.9506-2.01360.23291550.1918928908396
2.0136-2.08550.24071560.18459013916996
2.0855-2.1690.23631250.17539066919197
2.169-2.26770.2011450.16828970911597
2.2677-2.38720.19731340.16679048918297
2.3872-2.53680.1931510.17059043919497
2.5368-2.73260.23361420.17969073921597
2.7326-3.00740.22411510.17039073922497
3.0074-3.44230.18811460.15989067921398
3.4423-4.33560.16591290.13739143927298
4.3356-35.06410.16941370.14499069920697
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)
10.89650.4499-0.47861.2748-0.91352.22670.0221-0.0804-0.0135-0.0805-0.0408-0.035-0.0439-0.048-0.00540.13750.031-0.02780.1528-0.0120.1413-21.1044-0.497844.5439
24.22480.1068-0.41023.8187-1.12015.2011-0.112-0.1861-0.4743-0.3339-0.0472-0.35040.34510.32720.09820.16170.02850.03620.21630.05570.2398-1.0607-1.470132.342
30.49120.0256-0.43721.53520.27571.69750.329-0.04820.29830.0336-0.0568-0.0528-0.91540.1125-0.190.7463-0.05790.18130.1951-0.02930.3158-6.849432.812836.184
42.0558-0.38080.59692.0209-1.53291.4476-0.28110.8285-0.3884-0.44460.31060.3386-0.48870.2363-0.09770.54210.00010.15740.56460.0180.4561-38.754532.240325.9443
51.1857-0.3765-0.35660.796-0.18810.62750.1359-0.01940.08190.21460.01860.147-0.3818-0.0837-0.12440.66180.07140.1540.20150.00510.2786-25.560230.561444.3395
60.7513-0.07380.5932.1442-0.59043.16920.05730.0152-0.1944-0.09320.0138-0.05860.43140.1314-0.05240.3023-0.0737-0.01960.22230.0020.2912-10.3209-26.8757-2.3986
70.85150.15960.24292.0762-0.14142.58370.020.0663-0.0374-0.20050.01830.1360.1705-0.2351-0.02720.1425-0.0429-0.03140.1662-0.01320.1845-12.4785-12.2939-12.865
86.58261.4741-0.24050.8371-0.51686.7776-0.47450.9867-0.1963-1.4620.0628-0.22660.53470.65790.41570.6222-0.02110.04840.4343-0.00850.291821.778-15.2827-9.4216
90.78430.42430.37081.6568-0.23622.2859-0.01350.0529-0.0341-0.2238-0.0413-0.0352-0.0450.1210.02920.1683-0.005-0.01540.17230.00290.1963-6.9132-5.5329-8.1948
101.8068-0.03470.3931.1706-0.0691.28270.0261-0.03960.0372-0.0003-0.02950.0220.1219-0.11210.02230.188-0.01890.00040.1632-0.00490.2063-2.9547-12.7744.3098
112.98590.42110.51870.7848-0.07880.9601-0.00190.0416-0.20760.05590.0222-0.0780.22310.0457-0.02930.2625-0.0075-0.00690.1107-0.00210.19425.36-23.5776.9747
124.2242-0.547-1.33916.05360.4746.325-0.0024-0.03420.07010.0743-0.0222-0.3367-0.00880.5626-0.01450.14560.0116-0.03950.14330.01940.201720.1671-14.60336.95
134.9519-1.2336-1.1182.2076-0.23420.88790.12370.23010.1694-0.1571-0.0118-0.1134-0.3646-0.0065-0.12720.2664-0.0282-0.01190.1707-0.02040.22995.998330.01837.0844
141.80650.0684-0.32292.41470.1831.4434-0.0180.01140.0321-0.150.0275-0.3334-0.11090.235-0.00120.1144-0.02870.00940.16540.00990.182717.883313.44430.5785
153.41050.2423-3.13582.6058-0.33478.76980.0530.27510.0396-0.39690.1161-0.3144-0.1785-0.036-0.15490.29330.00230.01540.24540.00220.2208-9.379414.9876-21.9675
161.0009-0.2536-0.21670.95030.1221.11930.0090.0107-0.0274-0.0667-0.04010.0676-0.0818-0.05820.00920.1178-0.0068-0.01580.11930.00080.1457-0.038914.28824.7081
174.1702-1.0166-0.38654.0412-0.48336.79020.0526-0.0520.2967-0.2330.05180.0383-0.6954-0.454-0.08640.21780.0268-0.02120.2191-0.0260.1693-17.291618.2556-10.3215
184.5733-1.57411.96762.3492-0.88063.75090.09110.314-0.2085-0.86040.05780.26670.5253-0.1348-0.23170.4331-0.0382-0.06630.2154-0.00820.3037-28.0884-15.148440.7059
192.2574-0.01170.35282.0935-0.51821.56470.09580.1478-0.0376-0.5150.15650.476-0.0321-0.6333-0.12540.28080.0681-0.13370.42040.04490.2604-38.01012.283233.4258
202.7146-0.8357-1.67370.24970.57441.23410.12620.40490.0223-0.2458-0.08050.0177-0.3253-0.2992-0.05620.35640.03130.00670.3030.010.2244-13.73435.868521.3108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 182 through 300 )C182 - 300
2X-RAY DIFFRACTION2chain 'C' and (resid 301 through 356 )C301 - 356
3X-RAY DIFFRACTION3chain 'D' and (resid -4 through 133 )D-4 - 133
4X-RAY DIFFRACTION4chain 'D' and (resid 134 through 164 )D134 - 164
5X-RAY DIFFRACTION5chain 'D' and (resid 165 through 356 )D165 - 356
6X-RAY DIFFRACTION6chain 'A' and (resid -6 through 35 )A-6 - 35
7X-RAY DIFFRACTION7chain 'A' and (resid 36 through 133 )A36 - 133
8X-RAY DIFFRACTION8chain 'A' and (resid 134 through 164 )A134 - 164
9X-RAY DIFFRACTION9chain 'A' and (resid 165 through 194 )A165 - 194
10X-RAY DIFFRACTION10chain 'A' and (resid 195 through 257 )A195 - 257
11X-RAY DIFFRACTION11chain 'A' and (resid 258 through 322 )A258 - 322
12X-RAY DIFFRACTION12chain 'A' and (resid 323 through 356 )A323 - 356
13X-RAY DIFFRACTION13chain 'B' and (resid -2 through 22 )B-2 - 22
14X-RAY DIFFRACTION14chain 'B' and (resid 23 through 134 )B23 - 134
15X-RAY DIFFRACTION15chain 'B' and (resid 135 through 164 )B135 - 164
16X-RAY DIFFRACTION16chain 'B' and (resid 165 through 300 )B165 - 300
17X-RAY DIFFRACTION17chain 'B' and (resid 301 through 356 )B301 - 356
18X-RAY DIFFRACTION18chain 'C' and (resid -2 through 22 )C-2 - 22
19X-RAY DIFFRACTION19chain 'C' and (resid 23 through 132 )C23 - 132
20X-RAY DIFFRACTION20chain 'C' and (resid 133 through 181 )C133 - 181

+
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