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- PDB-3bb5: CRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN OF UNKNOWN... -

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Basic information

Entry
Database: PDB / ID: 3bb5
TitleCRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN OF UNKNOWN FUNCTION (JANN_3925) FROM JANNASCHIA SP. CCS1 AT 2.30 A RESOLUTION
ComponentsStress responsive alpha-beta protein
KeywordsUNKNOWN FUNCTION / DIMERIC FERREDOXIN-LIKE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Stress responsive alpha-beta
Similarity search - Component
Biological speciesJannaschia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of dimeric ferredoxin-like protein of unknown function (YP_511867.1) from Jannaschia sp. CCS1 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 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 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 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: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Stress responsive alpha-beta protein
B: Stress responsive alpha-beta protein
C: Stress responsive alpha-beta protein
D: Stress responsive alpha-beta protein
E: Stress responsive alpha-beta protein
F: Stress responsive alpha-beta protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,64915
Polymers83,4406
Non-polymers1,2099
Water3,153175
1
A: Stress responsive alpha-beta protein
B: Stress responsive alpha-beta protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0684
Polymers27,8132
Non-polymers2542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
MethodPISA
2
C: Stress responsive alpha-beta protein
D: Stress responsive alpha-beta protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2605
Polymers27,8132
Non-polymers4463
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
MethodPISA
3
E: Stress responsive alpha-beta protein
F: Stress responsive alpha-beta protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3226
Polymers27,8132
Non-polymers5084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.721, 66.323, 110.452
Angle α, β, γ (deg.)90.000, 93.410, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 1 - 102 / Label seq-ID: 20 - 121

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein
Stress responsive alpha-beta protein


Mass: 13906.662 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Jannaschia sp. (bacteria) / Strain: CCS1 / Gene: YP_511867.1, Jann_3925 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q28KC0
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsREMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG.

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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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: NANODROP, 10.0% PEG 6000, 0.1M Citrate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537, 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97951
ReflectionResolution: 2.3→29.841 Å / Num. obs: 47632 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 40.54 Å2 / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.363.70.9070.81286434690.907100
2.36-2.423.70.6881.11277134150.688100
2.42-2.493.70.6071.21231332940.607100
2.49-2.573.70.5111.41213832530.511100
2.57-2.663.70.4231.71163631180.423100
2.66-2.753.70.36821135330520.368100
2.75-2.853.70.2772.71088429100.277100
2.85-2.973.70.2143.41048528230.214100
2.97-3.13.70.1664.31003226990.16699.9
3.1-3.253.70.1265.6970826200.12699.9
3.25-3.433.70.0947892124160.09499.9
3.43-3.643.70.0798.4856623350.079100
3.64-3.893.60.0729.3807522170.072100
3.89-4.23.60.0699.4730720390.069100
4.2-4.63.60.0610.7670918890.06100
4.6-5.143.50.06310600517190.063100
5.14-5.943.30.0699.1503815090.069100
5.94-7.273.30.06310.4431212920.06399.9
7.27-10.293.60.05511.6359810090.055100
10.29-29.8413.40.04712.218745540.04795.8

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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
ADSCQuantumdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.841 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / SU B: 11.815 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.187 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. CITRATE AND ETHYLENE GLYCOL ARE MODELED BASED ON THE CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2409 5.1 %RANDOM
Rwork0.179 ---
obs0.181 47622 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.854 Å2
Baniso -1Baniso -2Baniso -3
1-2.39 Å20 Å20.56 Å2
2---0.11 Å20 Å2
3----2.21 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4756 0 81 175 5012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224950
X-RAY DIFFRACTIONr_bond_other_d0.0010.023314
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9966701
X-RAY DIFFRACTIONr_angle_other_deg0.96938052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8465624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.58223.514222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51315779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4261535
X-RAY DIFFRACTIONr_chiral_restr0.0840.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025613
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02998
X-RAY DIFFRACTIONr_nbd_refined0.1960.2981
X-RAY DIFFRACTIONr_nbd_other0.1840.23428
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22313
X-RAY DIFFRACTIONr_nbtor_other0.0890.22521
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3190.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.25
X-RAY DIFFRACTIONr_mcbond_it1.98733223
X-RAY DIFFRACTIONr_mcbond_other0.63331275
X-RAY DIFFRACTIONr_mcangle_it2.7554918
X-RAY DIFFRACTIONr_scbond_it4.98381959
X-RAY DIFFRACTIONr_scangle_it7.062111780
Refine LS restraints NCS

Ens-ID: 1 / Number: 1273 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.560.5
2BMEDIUM POSITIONAL0.470.5
3CMEDIUM POSITIONAL0.550.5
4DMEDIUM POSITIONAL0.580.5
5EMEDIUM POSITIONAL0.530.5
6FMEDIUM POSITIONAL0.590.5
1AMEDIUM THERMAL1.082
2BMEDIUM THERMAL1.012
3CMEDIUM THERMAL1.022
4DMEDIUM THERMAL0.992
5EMEDIUM THERMAL1.072
6FMEDIUM THERMAL0.982
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 165 -
Rwork0.268 3278 -
all-3443 -
obs--99.77 %
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)
13.22220.36451.85441.4604-0.8372.21980.11430.15020.0293-0.127-0.0825-0.01470.06390.2527-0.0318-0.04540.09470.01110.02820.0044-0.1647-16.157-84.264-26.817
22.47510.9171.28582.66980.21552.97620.01070.05550.034-0.04160.0433-0.0420.09-0.0355-0.054-0.13490.03250.0415-0.03960.014-0.1628-9.142-82.667-9.103
31.26650.1033-1.21432.57070.15023.98510.0118-0.0441-0.09040.10980.03050.1027-0.0887-0.1312-0.0423-0.02380.05860.0167-0.10970.0079-0.1777-45.355-64.807-27.548
41.8049-0.9032-1.24852.89250.67543.64780.0429-0.18610.0627-0.1111-0.0485-0.2514-0.01060.18690.0056-0.06830.03250.0273-0.00650.0154-0.1648-48.561-57.146-10.954
51.4632-0.2408-0.73051.49081.10354.4457-0.037-0.0181-0.006-0.04180.06220.06260.04550.1758-0.0252-0.10370.0578-0.0196-0.10510.0034-0.1608-32.504-77.373-46.518
61.9072-0.0432-0.31542.09480.97773.8057-0.03940.00820.0685-0.29580.1009-0.1535-0.3230.2379-0.06160.0364-0.04170.0299-0.1027-0.0246-0.1685-24.806-79.572-63.858
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 10219 - 121
2X-RAY DIFFRACTION2BB0 - 10219 - 121
3X-RAY DIFFRACTION3CC0 - 10219 - 121
4X-RAY DIFFRACTION4DD-5 - 10214 - 121
5X-RAY DIFFRACTION5EE-1 - 10218 - 121
6X-RAY DIFFRACTION6FF0 - 10219 - 121

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