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- PDB-2op5: CRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN (JCVI_PEP_... -

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Basic information

Entry
Database: PDB / ID: 2op5
TitleCRYSTAL STRUCTURE OF A DIMERIC FERREDOXIN-LIKE PROTEIN (JCVI_PEP_1096672785533) FROM UNCULTURED MARINE ORGANISM AT 2.20 A RESOLUTION
Componentshypothetical protein
KeywordsOXIDOREDUCTASE / FERREDOXIN-LIKE PROTEIN / 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
Function and homology information
Biological speciesuncultured marine organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (JCVI_PEP_1096672785533) from an environmental metagenome (unidentified marine microbe), Sorcerer II Global Ocean Sampling experiment at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1, 2, 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 ... BIOMOLECULE: 1, 2, 3 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 6 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE (1) THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ... SEQUENCE (1) THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL 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 UNIPROT DATABASE AT THE TIME OF PROCESSING. (3) PRODUCT OF THE EXPRESSED SYNTHETIC GENE WAS BASED ON THE PREDICTED SEQUENCE OF ACCESSION ID JCVI_PEP_1096672785533 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
E: hypothetical protein
F: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,17715
Polymers83,6186
Non-polymers5599
Water2,900161
1
A: hypothetical protein
B: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1216
Polymers27,8732
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-5 kcal/mol
Surface area11370 Å2
MethodPISA
2
C: hypothetical protein
D: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9974
Polymers27,8732
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-5 kcal/mol
Surface area11510 Å2
MethodPISA
3
E: hypothetical protein
F: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0595
Polymers27,8732
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-4 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.558, 84.629, 144.952
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
21C
31E
41A
51B
61C
71D
81E
91F
101A
111B
121C
131D
141E
151F
161A
171B
181C
191D
201E
211F
221A
231B
241C
251D
261E
271F
281A
291B
301C
311D
321E
331F
341A
351B
361C
371D
381E
391F
401A
411B
421C
431D
441E
451F

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR6AA4 - 75 - 8
21GLYGLYTHRTHR6CC0 - 71 - 8
31ASPASPTHRTHR6EE5 - 76 - 8
42THRTHRLEULEU4AA7 - 258 - 26
52ALAALALEULEU4BB8 - 259 - 26
62THRTHRLEULEU4CC7 - 258 - 26
72ALAALALEULEU4DD8 - 259 - 26
82THRTHRLEULEU4EE7 - 258 - 26
92THRTHRLEULEU4FF7 - 258 - 26
103PHEPHEALAALA6AA26 - 4527 - 46
113PHEPHEALAALA6BB26 - 4527 - 46
123PHEPHEALAALA6CC26 - 4527 - 46
133PHEPHEALAALA6DD26 - 4527 - 46
143PHEPHEALAALA6EE26 - 4527 - 46
153PHEPHEALAALA6FF26 - 4527 - 46
164GLYGLYLYSLYS4AA46 - 5447 - 55
174GLYGLYLYSLYS4BB46 - 5447 - 55
184GLYGLYLYSLYS4CC46 - 5447 - 55
194GLYGLYLYSLYS4DD46 - 5447 - 55
204GLYGLYLYSLYS4EE46 - 5447 - 55
214GLYGLYLYSLYS4FF46 - 5447 - 55
225VALVALARGARG6AA55 - 6256 - 63
235VALVALARGARG6BB55 - 6256 - 63
245VALVALARGARG6CC55 - 6256 - 63
255VALVALARGARG6DD55 - 6256 - 63
265VALVALARGARG6EE55 - 6256 - 63
275VALVALARGARG6FF55 - 6256 - 63
286ILEILEGLNGLN4AA63 - 7964 - 80
296ILEILEGLNGLN4BB63 - 7964 - 80
306ILEILEGLNGLN4CC63 - 7964 - 80
316ILEILEGLNGLN4DD63 - 7964 - 80
326ILEILEGLNGLN4EE63 - 7964 - 80
336ILEILEGLNGLN4FF63 - 7964 - 80
347GLUGLULYSLYS6AA80 - 10081 - 101
357GLUGLULYSLYS6BB80 - 10081 - 101
367GLUGLULYSLYS6CC80 - 10081 - 101
377GLUGLULYSLYS6DD80 - 10081 - 101
387GLUGLULYSLYS6EE80 - 10081 - 101
397GLUGLULYSLYS6FF80 - 10081 - 101
408ILEILESERSER4AA101 - 115102 - 116
418ILEILESERSER4BB101 - 115102 - 116
428ILEILESERSER4CC101 - 115102 - 116
438ILEILEARGARG4DD101 - 114102 - 115
448ILEILESERSER4EE101 - 115102 - 116
458ILEILEARGARG4FF101 - 114102 - 115
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
hypothetical protein


Mass: 13936.413 Da / Num. of mol.: 6
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_1096672785533 from the Sorcerer II Global Ocean Sampling experiment
Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: NANODROP, 0.2M Potassium formate, 20.0% PEG 3350, No Buffer, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.94645, 0.97942, 0.97921
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.946451
20.979421
30.979211
ReflectionResolution: 2.2→48.34 Å / Num. obs: 36082 / % possible obs: 99.6 % / Biso Wilson estimate: 25.76 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.22
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allDiffraction-ID% possible all
2.2-2.280.6831.8127793630198.8
2.28-2.370.5932.2128733501199.9
2.37-2.480.492.6134033644199.9
2.48-2.610.393.2129653518199.9
2.61-2.770.323.9128413506199.9
2.77-2.980.245.3130303553199.9
2.98-3.280.1547.9132843634199.9
3.28-3.760.0912.2133683678199.8
3.76-4.720.06815.5129673648199.6
4.72-48.30.05616.3133683902198.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→48.34 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.855 / SU B: 17.953 / SU ML: 0.221 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.351 / ESU R Free: 0.264
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. MOLECULES OF ETHYLENE GLYCOL USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE. 5. A PSEUDO-TRANSLATION ALONG THE CRYSTALLOGRAPHIC C-AXIS BY (0,0,1/3) RELATES PAIRS OF DIMERS IN THE UNIT CELL. 6. ALTHOUGH THERE IS GENERAL AGREEMENT BETWEEN THE ELECTRON DENSITY MAPS AND THE MODEL MAPS, THE REASONS FOR THE ELEVATED R-FACTORS (R-WORK AND R-FREE) ARE NOT COMPLETELY UNDERSTOOD.
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1799 5 %RANDOM
Rwork0.23 ---
all0.233 ---
obs0.233 36027 99.67 %-
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: 27.408 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--1.26 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5307 0 36 161 5504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225503
X-RAY DIFFRACTIONr_bond_other_d0.0020.024993
X-RAY DIFFRACTIONr_angle_refined_deg1.511.9427393
X-RAY DIFFRACTIONr_angle_other_deg0.863311552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3675670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5224.212273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.613151002
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8681529
X-RAY DIFFRACTIONr_chiral_restr0.0850.2819
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026068
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021204
X-RAY DIFFRACTIONr_nbd_refined0.1830.31009
X-RAY DIFFRACTIONr_nbd_other0.1580.34920
X-RAY DIFFRACTIONr_nbtor_refined0.1830.52563
X-RAY DIFFRACTIONr_nbtor_other0.0850.53359
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1950.5328
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0280.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.382
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.522
X-RAY DIFFRACTIONr_mcbond_it0.90423449
X-RAY DIFFRACTIONr_mcbond_other0.21121365
X-RAY DIFFRACTIONr_mcangle_it1.37135286
X-RAY DIFFRACTIONr_scbond_it1.76442413
X-RAY DIFFRACTIONr_scangle_it2.56152097
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A789MEDIUM POSITIONAL0.680.5
5B789MEDIUM POSITIONAL0.650.5
2C789MEDIUM POSITIONAL0.750.5
7D789MEDIUM POSITIONAL0.730.5
3E789MEDIUM POSITIONAL0.670.5
9F789MEDIUM POSITIONAL0.610.5
1A659LOOSE POSITIONAL1.545
5B659LOOSE POSITIONAL1.345
2C659LOOSE POSITIONAL2.455
7D659LOOSE POSITIONAL2.175
3E659LOOSE POSITIONAL1.375
9F659LOOSE POSITIONAL1.315
1A789MEDIUM THERMAL0.632
5B789MEDIUM THERMAL0.642
2C789MEDIUM THERMAL0.632
7D789MEDIUM THERMAL0.642
3E789MEDIUM THERMAL0.632
9F789MEDIUM THERMAL0.562
1A659LOOSE THERMAL2.7710
5B659LOOSE THERMAL2.6510
2C659LOOSE THERMAL2.4210
7D659LOOSE THERMAL2.0810
3E659LOOSE THERMAL1.9410
9F659LOOSE THERMAL1.9810
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 125 -
Rwork0.284 2485 -
obs-2610 98.34 %
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)
13.54180.393-0.35240.94320.69933.17320.02690.0183-0.0005-0.0394-0.04540.01440.10380.10920.0185-0.1180.04110.0069-0.17860.0216-0.127824.14837.678625.3054
22.6717-1.78521.81241.4849-0.44956.5032-0.02210.00880.28230.0089-0.015-0.1081-0.54190.44090.037-0.0943-0.03820.0399-0.1231-0.0212-0.042232.544317.533241.0553
32.92870.48161.10951.42880.20474.3857-0.12710.08670.1489-0.05370.09040.0187-0.0727-0.24910.0366-0.11760.00180.0325-0.1587-0.0096-0.10464.329-5.73641.7592
42.3012-1.2462-1.27924.88821.78413.5299-0.0839-0.1325-0.1840.16880.0260.14040.1455-0.21370.0579-0.1620.002-0.0177-0.11640.0201-0.1018-6.9196-12.759316.8334
53.86280.04020.72131.9527-0.93443.1714-0.0205-0.0524-0.0304-0.09210.05540.05360.0113-0.1113-0.035-0.1157-0.00230.008-0.1993-0.0334-0.15431.2655-1.952150.0313
60.8229-0.00480.03382.53221.63925.36130.0313-0.14550.06570.1746-0.05820.11390.1502-0.20180.0269-0.1851-0.0326-0.0324-0.0404-0.0206-0.031-5.769-15.204164.4683
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 1155 - 116
22BB8 - 1159 - 116
33CC0 - 1151 - 116
44DD8 - 1149 - 115
55EE5 - 1156 - 116
66FF7 - 1148 - 115

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