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- PDB-5d4p: Structure of CPII bound to ADP and bicarbonate, from Thiomonas in... -

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Basic information

Entry
Database: PDB / ID: 5d4p
TitleStructure of CPII bound to ADP and bicarbonate, from Thiomonas intermedia K12
ComponentsPutative Nitrogen regulatory protein P-II GlnB
KeywordsSIGNALING PROTEIN / carbon regulatory PII protein / CPII / nitrogen regulatory PII protein / nucleotide binding / ADP hydrolysis / bicarbonate binding / acetate binding
Function / homology
Function and homology information


regulation of nitrogen utilization / enzyme regulator activity / nucleotide binding
Similarity search - Function
Nitrogen regulatory protein P-II / Nitrogen regulatory protein PII / P-II protein family profile. / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BICARBONATE ION / Nitrogen regulatory protein P-II / Putative Nitrogen regulatory protein P-II GlnB
Similarity search - Component
Biological speciesThiomonas arsenitoxydans
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
Model detailsnitrogen regulatory PII superfamily protein
AuthorsWheatley, N.M. / Ngo, J. / Cascio, D. / Sawaya, M.R. / Yeates, T.O.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: A PII-Like Protein Regulated by Bicarbonate: Structural and Biochemical Studies of the Carboxysome-Associated CPII Protein.
Authors: Wheatley, N.M. / Eden, K.D. / Ngo, J. / Rosinski, J.S. / Sawaya, M.R. / Cascio, D. / Collazo, M. / Hoveida, H. / Hubbell, W.L. / Yeates, T.O.
History
DepositionAug 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Nitrogen regulatory protein P-II GlnB
B: Putative Nitrogen regulatory protein P-II GlnB
C: Putative Nitrogen regulatory protein P-II GlnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,56113
Polymers35,8533
Non-polymers1,70910
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-31 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.810, 76.160, 87.920
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ARG / End label comp-ID: ARG

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ALAALAchain AAA3 - 1073 - 107
2ILEILEchain BBB4 - 1074 - 107
3ASNASNchain CCC2 - 1072 - 107

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Components

#1: Protein Putative Nitrogen regulatory protein P-II GlnB


Mass: 11950.863 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thiomonas arsenitoxydans (strain DSM 22701 / CIP 110005 / 3As) (bacteria)
Strain: DSM 22701 / CIP 110005 / 3As / Gene: THI_0133 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D5X329, UniProt: D6CQJ8*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8 / Details: 1.0 M Citrate, 0.1 M imidazole pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→57.57 Å / Num. obs: 17217 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 5.74 % / Biso Wilson estimate: 34.24 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.085 / Χ2: 0.962 / Net I/σ(I): 14.98 / Num. measured all: 98900
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.260.8860.5972.966227128111770.65891.9
2.26-2.320.9020.6172.967106123612040.67697.4
2.32-2.380.940.4443.817250121712110.48599.5
2.38-2.460.9630.3814.37033118111780.41799.7
2.46-2.540.9640.315.276683114811400.3499.3
2.54-2.630.9730.2626.246521111510990.28798.6
2.63-2.730.9790.2177.255999105310450.23999.2
2.73-2.840.9840.1948.075343104410310.21698.8
2.84-2.960.9910.13811.5858989949890.15299.5
2.96-3.110.9930.10614.3756949409340.11699.4
3.11-3.280.9960.0818.3754419149100.08899.6
3.28-3.480.9960.06622.6950548638530.07398.8
3.48-3.720.9970.05926.4444878187940.06597.1
3.72-4.010.9970.05227.9639277607390.05897.2
4.01-4.40.9990.03933.2635917066760.04395.8
4.4-4.920.9990.03440.2437366456380.03798.9
4.92-5.680.9980.03637.1832195725670.0499.1
5.68-6.950.9980.03834.2927235004890.04297.8
6.95-9.830.9990.03539.8118213903450.03888.5
9.8310.03150.6611472351980.03384.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å43.34 Å
Translation2.2 Å43.34 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D4L

5d4l


Resolution: 2.2→43.338 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 1718 9.99 %
Rwork0.1912 15476 -
obs0.1968 17194 97.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.62 Å2 / Biso mean: 43.9004 Å2 / Biso min: 19.77 Å2
Refinement stepCycle: final / Resolution: 2.2→43.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 124 45 2510
Biso mean--40.95 44.2 -
Num. residues----312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082501
X-RAY DIFFRACTIONf_angle_d1.283391
X-RAY DIFFRACTIONf_chiral_restr0.052376
X-RAY DIFFRACTIONf_plane_restr0.006420
X-RAY DIFFRACTIONf_dihedral_angle_d17.696880
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1388X-RAY DIFFRACTION11.455TORSIONAL
12B1388X-RAY DIFFRACTION11.455TORSIONAL
13C1388X-RAY DIFFRACTION11.455TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.26310.47121300.42011174130491
2.2631-2.33610.4031400.31271261140198
2.3361-2.41960.28321430.220812861429100
2.4196-2.51650.26171460.20331306145299
2.5165-2.6310.34741440.21151297144199
2.631-2.76970.27921420.21951290143299
2.7697-2.94320.30611450.21321300144599
2.9432-3.17040.26141440.213812961440100
3.1704-3.48930.241450.20041318146399
3.4893-3.99390.21021430.16531291143497
3.9939-5.03070.18151460.12651314146097
5.0307-43.34660.20951500.16961343149394
Refinement TLS params.Method: refined / Origin x: -3.9521 Å / Origin y: 1.1362 Å / Origin z: -7.4624 Å
111213212223313233
T0.2092 Å20.0019 Å20.0085 Å2-0.3516 Å2-0.0203 Å2--0.1663 Å2
L1.6893 °20.3224 °20.5403 °2-2.3328 °2-0.063 °2--3.3954 °2
S0.0075 Å °0.0807 Å °-0.0646 Å °-0.1252 Å °0.0481 Å °-0.0452 Å °0.013 Å °0.1061 Å °-0.062 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:107 OR RESID 201:201 OR RESID 301:314 OR RESID 202:202 ) ) OR ( CHAIN C AND ( RESID 2:107 OR RESID 201:201 OR RESID 301:322 OR RESID 202:204 ) ) OR ( CHAIN B AND ( RESID 4:107 OR RESID 201:201 OR RESID 301:309 OR RESID 202:204 ) )A3 - 107
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:107 OR RESID 201:201 OR RESID 301:314 OR RESID 202:202 ) ) OR ( CHAIN C AND ( RESID 2:107 OR RESID 201:201 OR RESID 301:322 OR RESID 202:204 ) ) OR ( CHAIN B AND ( RESID 4:107 OR RESID 201:201 OR RESID 301:309 OR RESID 202:204 ) )A201
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:107 OR RESID 201:201 OR RESID 301:314 OR RESID 202:202 ) ) OR ( CHAIN C AND ( RESID 2:107 OR RESID 201:201 OR RESID 301:322 OR RESID 202:204 ) ) OR ( CHAIN B AND ( RESID 4:107 OR RESID 201:201 OR RESID 301:309 OR RESID 202:204 ) )A301 - 314
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:107 OR RESID 201:201 OR RESID 301:314 OR RESID 202:202 ) ) OR ( CHAIN C AND ( RESID 2:107 OR RESID 201:201 OR RESID 301:322 OR RESID 202:204 ) ) OR ( CHAIN B AND ( RESID 4:107 OR RESID 201:201 OR RESID 301:309 OR RESID 202:204 ) )A202
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:107 OR RESID 201:201 OR RESID 301:314 OR RESID 202:202 ) ) OR ( CHAIN C AND ( RESID 2:107 OR RESID 201:201 OR RESID 301:322 OR RESID 202:204 ) ) OR ( CHAIN B AND ( RESID 4:107 OR RESID 201:201 OR RESID 301:309 OR RESID 202:204 ) )C2 - 107
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:107 OR RESID 201:201 OR RESID 301:314 OR RESID 202:202 ) ) OR ( CHAIN C AND ( RESID 2:107 OR RESID 201:201 OR RESID 301:322 OR RESID 202:204 ) ) OR ( CHAIN B AND ( RESID 4:107 OR RESID 201:201 OR RESID 301:309 OR RESID 202:204 ) )C201
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:107 OR RESID 201:201 OR RESID 301:314 OR RESID 202:202 ) ) OR ( CHAIN C AND ( RESID 2:107 OR RESID 201:201 OR RESID 301:322 OR RESID 202:204 ) ) OR ( CHAIN B AND ( RESID 4:107 OR RESID 201:201 OR RESID 301:309 OR RESID 202:204 ) )C301 - 322
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:107 OR RESID 201:201 OR RESID 301:314 OR RESID 202:202 ) ) OR ( CHAIN C AND ( RESID 2:107 OR RESID 201:201 OR RESID 301:322 OR RESID 202:204 ) ) OR ( CHAIN B AND ( RESID 4:107 OR RESID 201:201 OR RESID 301:309 OR RESID 202:204 ) )C202 - 204
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:107 OR RESID 201:201 OR RESID 301:314 OR RESID 202:202 ) ) OR ( CHAIN C AND ( RESID 2:107 OR RESID 201:201 OR RESID 301:322 OR RESID 202:204 ) ) OR ( CHAIN B AND ( RESID 4:107 OR RESID 201:201 OR RESID 301:309 OR RESID 202:204 ) )B4 - 107
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:107 OR RESID 201:201 OR RESID 301:314 OR RESID 202:202 ) ) OR ( CHAIN C AND ( RESID 2:107 OR RESID 201:201 OR RESID 301:322 OR RESID 202:204 ) ) OR ( CHAIN B AND ( RESID 4:107 OR RESID 201:201 OR RESID 301:309 OR RESID 202:204 ) )B201
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:107 OR RESID 201:201 OR RESID 301:314 OR RESID 202:202 ) ) OR ( CHAIN C AND ( RESID 2:107 OR RESID 201:201 OR RESID 301:322 OR RESID 202:204 ) ) OR ( CHAIN B AND ( RESID 4:107 OR RESID 201:201 OR RESID 301:309 OR RESID 202:204 ) )B301 - 309
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:107 OR RESID 201:201 OR RESID 301:314 OR RESID 202:202 ) ) OR ( CHAIN C AND ( RESID 2:107 OR RESID 201:201 OR RESID 301:322 OR RESID 202:204 ) ) OR ( CHAIN B AND ( RESID 4:107 OR RESID 201:201 OR RESID 301:309 OR RESID 202:204 ) )B202 - 204

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