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- PDB-2od6: Crystal structure of a dimeric ferredoxin-like protein (jcvi_pep_... -

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Entry
Database: PDB / ID: 2od6
TitleCrystal structure of a dimeric ferredoxin-like protein (jcvi_pep_1096682647733) from uncultured marine organism at 1.85 A resolution
Componentshypothetical protein
KeywordsUNKNOWN FUNCTION / Metagenomics target / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyAlpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / 10-oxohexadecanoic acid
Function and homology information
Biological speciesuncultured marine organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (JCVI_PEP_1096682647733) from an environmental metagenome (unidentified marine microbe), Sorcerer II Global Ocean Sampling experiment at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / 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 1.5Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...BIOMOLECULE: 1,2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE (1) THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE (1) 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. (2) THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE IN THE UNP DATABASE AT THE TIME OF PROCESSING. (3) PRODUCT OF THE EXPRESSED SYNTHETIC GENE WAS BASED ON THE PREDICTED SEQUENCE OF ACCESSION ID JCVI_PEP_1096682647733 FROM THE J. CRAIG VENTER INSTITUTE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
C: hypothetical protein
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,67719
Polymers51,9124
Non-polymers1,76415
Water5,423301
1
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7458
Polymers25,9562
Non-polymers7896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-4 kcal/mol
Surface area12460 Å2
MethodPISA
2
C: hypothetical protein
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,93111
Polymers25,9562
Non-polymers9759
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint1 kcal/mol
Surface area11980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.433, 92.842, 144.927
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
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: OHA / End label comp-ID: OHA / Refine code: 6 / Auth seq-ID: 3 - 300 / Label seq-ID: 4

Dom-IDAuth asym-IDLabel asym-ID
1AA - E
2BB - G
3CC - K
4DD - O
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
hypothetical protein /


Mass: 12978.046 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured marine organism (environmental samples)
Description: SYNTHETIC GENE: The gene product was based on JCVI_PEP_1096682647733 from the Sorcerer II Global Ocean Sampling experiment
Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-OHA / 10-oxohexadecanoic acid


Mass: 270.408 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H30O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.36 Å3/Da / Density % sol: 47.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9
Details: 30.0% PEG-6000, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97944, 0.97972
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 19, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979441
30.979721
ReflectionResolution: 1.8→29.086 Å / Num. obs: 42961 / % possible obs: 99.8 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 6.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.93.60.6111.21129731340.611100
1.9-1.953.60.4441.71099730520.444100
1.95-2.013.60.36821075129760.368100
2.01-2.073.60.2922.51039528850.292100
2.07-2.143.60.2422.91015228210.242100
2.14-2.213.60.1863.7972526900.186100
2.21-2.293.60.1753.9941926300.175100
2.29-2.393.60.1424.7915325410.142100
2.39-2.493.60.1195.5872224280.119100
2.49-2.623.60.1075.6842223570.107100
2.62-2.763.60.0976.3789922060.097100
2.76-2.933.60.0886747521030.088100
2.93-3.133.60.0767.5711320010.076100
3.13-3.383.50.0677.8655618540.067100
3.38-3.73.50.05510.6611117280.055100
3.7-4.143.50.04911.8546415600.04999.9
4.14-4.783.50.04912.4481413860.04999.7
4.78-5.853.40.04812.7409511950.04899.4
5.85-8.273.30.04912.330879320.04998.8
8.27-29.092.90.04214.914024820.04286.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.85→29.086 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 9.082 / SU ML: 0.132 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.137
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. (2). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (3). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING ...Details: (1). HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. (2). ATOM RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (4). RESIDUES 85-88 IN A SUBUNIT ARE DISORDERED. THE GEOMETRY IS POOR IN THIS REGION. (5). 10-KETO PALMITIC ACIDS (10-OXO-HEXADECANOIC ACID; OHA) WERE MODELLED IN THE ACTIVE SITE POCKETS. THE CARBOXYL GROUPS OF THE HEAD GROUPS OF THE FATTY ACIDS INTERACT WITH THE SIDE CHAINS OF SER 8, TYR 66, ARG 102 AND TYR 64. THE OHA ASSOCIATED WITH CHAIN C HAS THE BEST DENSITY. THE ASSIGNMENT OF THE FATTY ACIDS WAS BASED ON ELECTRON DENSITY AND THE STRUCTURAL SIMILARITY WITH OTHER MONOOXYGENASES. THEY COULD BE OTHER SIMILAR LIPIDS.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2164 5 %RANDOM
Rwork0.197 ---
obs0.198 42910 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.009 Å2
Baniso -1Baniso -2Baniso -3
1-4.05 Å20 Å20 Å2
2---2.58 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 120 301 3889
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223833
X-RAY DIFFRACTIONr_bond_other_d0.0010.022645
X-RAY DIFFRACTIONr_angle_refined_deg1.6811.9645171
X-RAY DIFFRACTIONr_angle_other_deg1.06136445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7535466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35323.879165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26715647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6321520
X-RAY DIFFRACTIONr_chiral_restr0.1360.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024221
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02827
X-RAY DIFFRACTIONr_nbd_refined0.2130.2756
X-RAY DIFFRACTIONr_nbd_other0.1970.22737
X-RAY DIFFRACTIONr_nbtor_refined0.190.21821
X-RAY DIFFRACTIONr_nbtor_other0.0930.22085
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.213
X-RAY DIFFRACTIONr_mcbond_it2.46532336
X-RAY DIFFRACTIONr_mcbond_other0.7163901
X-RAY DIFFRACTIONr_mcangle_it3.12253731
X-RAY DIFFRACTIONr_scbond_it5.68181698
X-RAY DIFFRACTIONr_scangle_it6.948111440
Refine LS restraints NCS

Ens-ID: 1 / Number: 1265 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.735
2BLOOSE POSITIONAL0.555
3CLOOSE POSITIONAL0.675
4DLOOSE POSITIONAL0.645
1ALOOSE THERMAL5.0810
2BLOOSE THERMAL2.9810
3CLOOSE THERMAL4.3610
4DLOOSE THERMAL3.6610
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 174 -
Rwork0.287 2956 -
obs-3130 100 %
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)
10.2499-0.0787-0.1232.6544-0.1413.1537-0.0939-0.01350.06350.45520.0720.3304-0.0916-0.24620.0219-0.1434-0.0039-0.0011-0.0225-0.0142-0.034918.122850.508422.0082
20.8985-1.0984-0.01142.2480.66080.4623-0.0856-0.0481-0.13050.2230.01790.08790.18780.06170.06770.0332-0.02010.0037-0.0920.013-0.063426.312433.364114.1724
31.10970.08780.38394.10710.94252.4647-0.03570.1026-0.1055-0.28430.09340.34630.4808-0.0374-0.0577-0.17850.0202-0.0342-0.0337-0.0065-0.019931.00333.295850.0967
40.63260.25560.19272.21270.61951.0826-0.06740.04460.0174-0.18480.0310.0198-0.21080.07520.03640.0198-0.00530.0045-0.08730.0206-0.090736.904451.77758.1371
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 109
2X-RAY DIFFRACTION2B2 - 109
3X-RAY DIFFRACTION3C3 - 109
4X-RAY DIFFRACTION4D2 - 109

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