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- PDB-6mmo: Carbon regulatory PII-like protein SbtB from Cyanobium sp. 7001 b... -

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Basic information

Entry
Database: PDB / ID: 6mmo
TitleCarbon regulatory PII-like protein SbtB from Cyanobium sp. 7001 bound to AMP
ComponentsCarbon regulatory PII-like protein SbtB
KeywordsSIGNALING PROTEIN / PII-like protein / SbtB / regulatory protein
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
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 MONOPHOSPHATE / Nitrogen regulatory protein P-II
Similarity search - Component
Biological speciesCyanobium sp. PCC 7001 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsKaczmarski, J.A. / Jackson, C.
CitationJournal: Biorxiv / Year: 2019
Title: Structure and function of SbtB from Cyanobium sp. 7001
Authors: Jackson, C. / Kaczmarski, J.A. / Price, D.
History
DepositionOct 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_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_alt_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbon regulatory PII-like protein SbtB
B: Carbon regulatory PII-like protein SbtB
C: Carbon regulatory PII-like protein SbtB
D: Carbon regulatory PII-like protein SbtB
E: Carbon regulatory PII-like protein SbtB
F: Carbon regulatory PII-like protein SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,19320
Polymers68,9046
Non-polymers2,28914
Water97354
1
A: Carbon regulatory PII-like protein SbtB
B: Carbon regulatory PII-like protein SbtB
D: Carbon regulatory PII-like protein SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,65112
Polymers34,4523
Non-polymers1,1999
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-70 kcal/mol
Surface area11800 Å2
MethodPISA
2
C: Carbon regulatory PII-like protein SbtB
E: Carbon regulatory PII-like protein SbtB
F: Carbon regulatory PII-like protein SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5428
Polymers34,4523
Non-polymers1,0905
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-39 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.737, 51.332, 66.803
Angle α, β, γ (deg.)97.91, 102.55, 103.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Carbon regulatory PII-like protein SbtB


Mass: 11484.044 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanobium sp. PCC 7001 (bacteria) / Gene: CPCC7001_1671 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5II98
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium Acetate 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.86→43.22 Å / Num. obs: 47208 / % possible obs: 97.1 % / Redundancy: 3.6 % / Net I/σ(I): 9.1
Reflection shellResolution: 1.86→1.9 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→43.221 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 35.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2518 2350 4.99 %
Rwork0.2099 --
obs0.2121 47131 96.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→43.221 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4061 0 146 54 4261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134351
X-RAY DIFFRACTIONf_angle_d1.2315910
X-RAY DIFFRACTIONf_dihedral_angle_d5.9763518
X-RAY DIFFRACTIONf_chiral_restr0.077709
X-RAY DIFFRACTIONf_plane_restr0.006703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.8980.44771310.47052572X-RAY DIFFRACTION95
1.898-1.93920.43181340.40322611X-RAY DIFFRACTION96
1.9392-1.98430.34041320.34562599X-RAY DIFFRACTION97
1.9843-2.0340.33411490.2982680X-RAY DIFFRACTION97
2.034-2.0890.33521320.2972604X-RAY DIFFRACTION97
2.089-2.15040.32071250.28132653X-RAY DIFFRACTION97
2.1504-2.21980.29411260.25142662X-RAY DIFFRACTION97
2.2198-2.29920.32531430.24842629X-RAY DIFFRACTION97
2.2992-2.39120.30921410.2292648X-RAY DIFFRACTION98
2.3912-2.50.30391500.23062646X-RAY DIFFRACTION97
2.5-2.63180.34251570.2452641X-RAY DIFFRACTION98
2.6318-2.79670.3061350.24722679X-RAY DIFFRACTION98
2.7967-3.01260.35511470.25232659X-RAY DIFFRACTION98
3.0126-3.31560.2991240.22262661X-RAY DIFFRACTION98
3.3156-3.79520.23981450.19792619X-RAY DIFFRACTION97
3.7952-4.78060.18191310.16392609X-RAY DIFFRACTION96
4.7806-43.23280.20631480.18042609X-RAY DIFFRACTION96

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