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- PDB-4qq7: Crystal Structure of Putative stringent starvation protein A from... -

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Basic information

Entry
Database: PDB / ID: 4qq7
TitleCrystal Structure of Putative stringent starvation protein A from Burkholderia cenocepacia with bound glutathione
ComponentsPutative stringent starvation protein A
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Glutaredoxin / Glutathione S-transferase
Function / homology
Function and homology information


Stringent starvation protein A, N-terminal / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Stringent starvation protein A, N-terminal / Glutathione S-transferase, N-terminal domain / Glutathione S-transferase, C-terminal domain / Glutathione transferase family / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase, C-terminal / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Soluble glutathione S-transferase N-terminal domain profile. / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, N-terminal / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
D-glucose / GLUTATHIONE / Putative stringent starvation protein A
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Putative stringent starvation protein A from Burkholderia cenocepacia with bound glutathione
Authors: Dranow, D.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D.
History
DepositionJun 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 stringent starvation protein A
B: Putative stringent starvation protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0556
Polymers48,0802
Non-polymers9754
Water2,054114
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-11 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.700, 95.200, 110.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid
21chain B and segid

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: SER / End label comp-ID: SER / Auth seq-ID: _ / Label seq-ID: 4

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and segidAA
2chain B and segidBB

NCS ensembles :
ID
1
2

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Components

#1: Protein Putative stringent starvation protein A


Mass: 24039.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: BCAL0331 / Production host: Escherichia coli (E. coli) / References: UniProt: B4E6Q3
#2: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N3O6S
#3: Sugar ChemComp-GLO / D-glucose / D-GLUCOSE IN LINEAR FORM


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus(F5): 10% PEG-20,000, 20% PEG-MME-550, 0.1M MOPS/HEPES-Na, pH7.5, 0.02M each D-glucose, D-galactose, D-mannose, L-fucose, D-xylose, N-acetyl-D-glucosamine, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 23, 2014
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 32307 / Num. obs: 32156 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 36.96 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 15.85
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.2-2.260.5542.76199.7
2.26-2.320.4573.28199.5
2.32-2.390.3773.97199.7
2.39-2.460.3254.49199.6
2.46-2.540.2635.45199.6
2.54-2.630.2196.29199.8
2.63-2.730.1956.45199.8
2.73-2.840.1597.47199.8
2.84-2.970.1279.231100
2.97-3.110.10611.05199.9
3.11-3.280.07316.5199.8
3.28-3.480.05622.59199.7
3.48-3.720.04229.49199.4
3.72-4.020.03533.56199.1
4.02-4.40.03138.37199.2
4.4-4.920.02843.2199.1
4.92-5.680.02541.01199.6
5.68-6.960.02340.93199.8
6.96-9.840.01750.58198.9
9.840.01554.76192.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.2 Å47.85 Å
Translation2.2 Å47.85 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.6phasing
PHENIXdev_1702refinement
PDB_EXTRACT3.14data extraction
JDirectordata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HOJ

4hoj


Resolution: 2.2→19.7 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 1549 4.84 %
Rwork0.1824 --
obs0.1842 32035 99.61 %
all-33584 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.9045 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3202 0 60 114 3376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093358
X-RAY DIFFRACTIONf_angle_d1.1824552
X-RAY DIFFRACTIONf_dihedral_angle_d13.7331260
X-RAY DIFFRACTIONf_chiral_restr0.056512
X-RAY DIFFRACTIONf_plane_restr0.006591
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1780X-RAY DIFFRACTION3.526TORSIONAL
12B1780X-RAY DIFFRACTION3.526TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.27090.3011530.27062719X-RAY DIFFRACTION100
2.2709-2.3520.26891240.23412735X-RAY DIFFRACTION100
2.352-2.4460.23351330.21632741X-RAY DIFFRACTION100
2.446-2.55710.30151360.21342740X-RAY DIFFRACTION100
2.5571-2.69160.23331220.21822744X-RAY DIFFRACTION100
2.6916-2.85980.31661380.2192772X-RAY DIFFRACTION100
2.8598-3.07980.27231490.21032760X-RAY DIFFRACTION100
3.0798-3.38830.2231350.20262778X-RAY DIFFRACTION100
3.3883-3.87540.20581330.16722796X-RAY DIFFRACTION99
3.8754-4.87030.1721500.13882806X-RAY DIFFRACTION99
4.8703-19.70030.19021760.15422895X-RAY DIFFRACTION99
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)
17.51271.681-3.27152.2958-3.42055.1930.2198-0.0672-0.03020.5364-0.09370.54560.1434-0.3827-0.09520.2976-0.0167-0.01940.3736-0.00750.235419.824264.581918.3581
23.12460.08961.02183.64520.14094.47820.1143-0.3813-0.16490.4573-0.14520.28440.4347-0.30770.05850.2636-0.010.03730.27380.03850.237223.520260.789415.8682
34.38051.22861.29729.07817.77578.71630.00140.3490.1891-0.4953-0.1815-0.33910.06110.73590.22470.43650.0974-0.00050.3560.12580.363339.521458.47675.7897
47.13880.58772.66926.578-1.45786.00130.2685-1.15320.01261.0361-0.1506-0.25370.0856-0.0003-0.18710.3869-0.0241-0.08910.55520.0270.300338.106372.045721.2019
54.52280.30351.86073.5661.01412.02510.1332-0.50320.27360.4578-0.0734-0.4850.07680.4555-0.16020.2797-0.0537-0.07280.36910.050.407243.881976.074912.3749
68.48955.3033-5.83198.3246-5.56574.7653-0.46820.7416-0.0992-0.73450.57030.27770.2636-0.3182-0.13920.283-0.0097-0.02660.37650.02310.276733.085567.0025-4.2617
73.47851.0254-0.33733.07350.44272.27410.06860.05750.39470.0048-0.018-0.0116-0.16420.0962-0.04530.17960.02520.00120.23430.03640.205834.481776.39445.7589
84.9269-3.2794-1.07175.67463.07093.0752-0.0922-0.20920.51620.00570.00020.2123-0.8854-0.20350.17060.26450.0066-0.02070.20660.00010.257122.497276.97029.1557
92.56190.38210.24295.659-0.49192.9004-0.07550.0036-0.5096-0.696-0.204-1.26660.16280.57180.2470.56950.17630.19180.57580.25450.807151.847845.66137.527
107.44522.5369-1.33924.2426-0.18723.0063-0.14390.3038-0.4439-1.0183-0.104-0.4810.36170.18640.24180.5710.17190.07920.34280.14270.442940.395946.16815.1718
116.2883.34615.18095.61813.12474.29960.2844-0.3853-0.23770.3748-0.50770.0880.28350.02790.19610.4593-0.0193-0.00890.40180.1220.440232.648350.027518.7076
121.7645-0.96732.07542.3283-0.3133.7090.3016-0.6613-0.09320.5888-0.7396-0.68340.30220.06430.34750.5878-0.113-0.0630.57330.30480.60143.626243.099927.2079
130.7961-0.3504-0.23951.106-0.27890.67610.0064-0.1524-0.1882-0.02-0.291-0.41780.31220.5193-0.05190.64870.2241-0.03150.59250.49961.066451.761634.130218.0215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 83 )
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 100 )
4X-RAY DIFFRACTION4chain 'A' and (resid 101 through 113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 139 )
6X-RAY DIFFRACTION6chain 'A' and (resid 140 through 150 )
7X-RAY DIFFRACTION7chain 'A' and (resid 151 through 185 )
8X-RAY DIFFRACTION8chain 'A' and (resid 186 through 203 )
9X-RAY DIFFRACTION9chain 'B' and (resid -1 through 51 )
10X-RAY DIFFRACTION10chain 'B' and (resid 52 through 83 )
11X-RAY DIFFRACTION11chain 'B' and (resid 84 through 100 )
12X-RAY DIFFRACTION12chain 'B' and (resid 101 through 185 )
13X-RAY DIFFRACTION13chain 'B' and (resid 186 through 202 )

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