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- PDB-2qea: CRYSTAL STRUCTURE OF A PUTATIVE GENERAL STRESS PROTEIN 26 (JANN_0... -

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Basic information

Entry
Database: PDB / ID: 2qea
TitleCRYSTAL STRUCTURE OF A PUTATIVE GENERAL STRESS PROTEIN 26 (JANN_0955) FROM JANNASCHIA SP. CCS1 AT 2.46 A RESOLUTION
ComponentsPutative general stress protein 26
KeywordsOXIDOREDUCTASE / PUTATIVE GENERAL STRESS PROTEIN 26 / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


General stress protein, FMN-binding split barrel domain / Pyridoxamine 5'-phosphate oxidase like / : / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
General stress protein 26
Similarity search - Component
Biological speciesJannaschia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.46 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative general stress protein 26 (YP_508897.1) from Jannaschia sp. CCS1 at 2.46 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 25, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.ptnr1_symmetry / _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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative general stress protein 26
B: Putative general stress protein 26
C: Putative general stress protein 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,65310
Polymers52,3733
Non-polymers2817
Water2,072115
1
A: Putative general stress protein 26
B: Putative general stress protein 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0756
Polymers34,9152
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-47 kcal/mol
Surface area15560 Å2
MethodPISA
2
C: Putative general stress protein 26
hetero molecules

C: Putative general stress protein 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1568
Polymers34,9152
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
3
C: Putative general stress protein 26
hetero molecules

C: Putative general stress protein 26
hetero molecules

A: Putative general stress protein 26
B: Putative general stress protein 26
hetero molecules

A: Putative general stress protein 26
B: Putative general stress protein 26
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,30620
Polymers104,7456
Non-polymers56114
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation10_675-y+1,-x+2,-z+5/61
identity operation1_555x,y,z1
crystal symmetry operation10_775-y+2,-x+2,-z+5/61
Buried area15690 Å2
ΔGint-213 kcal/mol
Surface area40740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.673, 73.673, 367.524
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHRAA5 - 356 - 36
21THRTHRTHRTHRBB5 - 356 - 36
31THRTHRTHRTHRCC5 - 356 - 36
42ALAALATHRTHRAA42 - 12843 - 129
52ALAALATHRTHRBB42 - 12843 - 129
62ALAALATHRTHRCC42 - 12843 - 129
73GLYGLYPHEPHEAA152 - 159153 - 160
83GLYGLYPHEPHEBB152 - 159153 - 160
93GLYGLYPHEPHECC152 - 159153 - 160
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative general stress protein 26


Mass: 17457.559 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jannaschia sp. (bacteria) / Strain: CCS1 / Gene: YP_508897.1, Jann_0955 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q28TU0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: NANODROP, 0.14M CaCl2, 30.0% Glycerol, 14.0% Isopropanol, 0.1M Acetate pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97905, 0.97920, 0.91837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 3, 2007 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979051
20.97921
30.918371
ReflectionResolution: 2.46→29.604 Å / Num. obs: 22684 / % possible obs: 99.8 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 5.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.46-2.523.60.7331572915880.73399.8
2.52-2.593.60.6311.1561015790.63199.8
2.59-2.676.70.6351.21045715600.635100
2.67-2.757.20.5651.31074514980.565100
2.75-2.847.10.4521.61043114760.452100
2.84-2.947.20.3152.41001313990.315100
2.94-3.0570.2842.6967813760.284100
3.05-3.187.10.2243.3941813200.224100
3.18-3.3270.1544.8886212750.154100
3.32-3.4870.1295.5855412250.129100
3.48-3.6770.1066.8821611800.106100
3.67-3.8970.098780111180.09100
3.89-4.166.80.0828.3717410540.082100
4.16-4.496.80.0788.567209870.078100
4.49-4.926.70.0738.762829400.073100
4.92-5.56.60.0749.154708320.074100
5.5-6.356.40.0769.249297680.076100
6.35-7.786.20.0768.341456640.07699.9
7.78-1160.05210.532125330.05298.4
11-29.6045.30.04711.116483120.04790.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.46→29.604 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.888 / SU B: 19.305 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.433 / ESU R Free: 0.287
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RESIDUES 38-39 IN CHAIN B ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 5. CA IONS FROM THE CRYSTALLIZATION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1159 5.1 %RANDOM
Rwork0.231 ---
obs0.233 22598 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.163 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.46→29.604 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3578 0 7 115 3700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223673
X-RAY DIFFRACTIONr_bond_other_d0.0020.022390
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9495000
X-RAY DIFFRACTIONr_angle_other_deg1.16935829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.7465474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.80225.116172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.46815537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.6411515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024244
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02747
X-RAY DIFFRACTIONr_nbd_refined0.1270.2539
X-RAY DIFFRACTIONr_nbd_other0.1170.22207
X-RAY DIFFRACTIONr_nbtor_refined0.1390.21751
X-RAY DIFFRACTIONr_nbtor_other0.0660.21716
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.040.2119
X-RAY DIFFRACTIONr_metal_ion_refined0.020.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.240
X-RAY DIFFRACTIONr_symmetry_vdw_other0.0950.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.030.212
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0360.21
X-RAY DIFFRACTIONr_mcbond_it0.63132478
X-RAY DIFFRACTIONr_mcbond_other0.0873981
X-RAY DIFFRACTIONr_mcangle_it1.09353731
X-RAY DIFFRACTIONr_scbond_it1.84681458
X-RAY DIFFRACTIONr_scangle_it2.71111268
Refine LS restraints NCS

Ens-ID: 1 / Number: 1556 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.455
2BLOOSE POSITIONAL0.335
3CLOOSE POSITIONAL0.395
1ALOOSE THERMAL1.3710
2BLOOSE THERMAL0.8910
3CLOOSE THERMAL1.0210
LS refinement shellResolution: 2.46→2.524 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 84 -
Rwork0.325 1495 -
obs-1579 99.68 %
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)
12.5397-0.82841.00392.7183-1.4453.5507-0.0588-0.12480.08710.17150.0456-0.1754-0.27840.10010.0132-0.1302-0.0002-0.0036-0.1513-0.0296-0.075442.234445.4706158.0804
21.80630.1380.80731.94860.82852.93530.0042-0.0116-0.0128-0.09160.02820.1777-0.0498-0.2553-0.0324-0.1231-0.01330.0004-0.12630.0455-0.055424.129945.5347150.9016
32.20640.2732-1.54330.842-0.65952.9215-0.0522-0.0574-0.1823-0.01250.0520.15810.2754-0.05220.0002-0.132-0.0112-0.0222-0.12470.0476-0.023547.80534.119155.6878
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 1591 - 160
2X-RAY DIFFRACTION2BB1 - 372 - 38
3X-RAY DIFFRACTION2BB40 - 15941 - 160
4X-RAY DIFFRACTION3CC1 - 1592 - 160

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