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Entry
Database: PDB / ID: 3dde
TitleCrystal structure of a domain of unknown function with a heme oxygenase-like fold (sden_3740) from shewanella denitrificans os217 at 2.30 A resolution
ComponentsTENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Iron-containing redox enzyme / Pyrroloquinoline-quinone synthase-like / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / TENA/THI-4 protein
Similarity search - Component
Biological speciesShewanella denitrificans OS217 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Domain of Unknown Function with a Heme Oxygenase-like Fold (YP_564736.1) from SHEWANELLA DENITRIFICANS OS-217 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 1.4Feb 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold
B: TENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3548
Polymers54,7622
Non-polymers5936
Water1,33374
1
A: TENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold
B: TENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold
hetero molecules

A: TENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold
B: TENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,70916
Polymers109,5234
Non-polymers1,18512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4630 Å2
ΔGint-34.8 kcal/mol
Surface area37820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.810, 66.000, 84.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERVAL2AA2 - 303 - 31
21SERVAL2BB2 - 303 - 31
32LEULYS6AA31 - 3432 - 35
42LEULYS6BB31 - 3432 - 35
53ALAALA2AA35 - 8436 - 85
63ALAALA2BB35 - 8436 - 85
74GLYGLY6AA8586
84GLYGLY6BB8586
95HISASP2AA86 - 10087 - 101
105HISASP2BB86 - 10087 - 101
116ARGARG6AA101102
126ARGARG6BB101102
137GLUALA2AA102 - 139103 - 140
147GLUALA2BB102 - 139103 - 140
158GLUTYR6AA140 - 145141 - 146
168GLUTYR6BB140 - 145141 - 146
179ILEPHE2AA146 - 167147 - 168
189ILEPHE2BB146 - 167147 - 168
1910ILELYS6AA168 - 176169 - 177
2010ILELYS6BB168 - 176169 - 177
2111HISHIS2AA177 - 186178 - 187
2211HISHIS2BB177 - 186178 - 187
2312GLUGLU6AA187188
2412GLUGLU6BB187188
2513VALTYR2AA188 - 220189 - 221
2613VALTYR2BB188 - 220189 - 221
2714GLNALA6AA221 - 232222 - 233
2814GLNALA6BB221 - 232222 - 233
DetailsAUTHORS STATE THAT THE PROTOMER MAY FORM A TETRAMER BASED ON CRYSTAL PACKING ANALYSIS. SIZE-EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein TENA/THI-4 protein, Domain of Unknown Function with a Heme Oxygenase-like Fold


Mass: 27380.824 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans OS217 (bacteria)
Gene: YP_564736.1, Sden_3740 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q12HR3

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Non-polymers , 5 types, 80 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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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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: 47.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20.0% polyethylene glycol 3350, 0.269M magnesium nitrate, NANODROP, 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: 0.91162,0.97932,0.97918
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 16, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979321
30.979181
ReflectionResolution: 2.3→29.173 Å / Num. obs: 23523 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.797 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 12.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.380.4331.97442388788.8
2.38-2.480.3322.58959464499
2.48-2.590.2423.48340431999
2.59-2.730.194.38826455298.9
2.73-2.90.1166.68550441999.2
2.9-3.120.0839.28396433499.2
3.12-3.430.0514.18479437298.8
3.43-3.930.03228732449698.7
3.93-4.930.02328.98508435598.3
4.930.0232.48693440796.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.173 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.924 / SU B: 17.745 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.37 / ESU R Free: 0.243
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. NITRATE, 1,2-ETHANEDIOL, PEG AND PGE WERE MODELED BASED ON CRYSTALLIZATION AND CRYOPROTECTION CONDITIONS. 5. AMINO ACID SER 225 IN CHAINS A AND B ARE RAMACHADRAN OUTLIERS IN A REGION OF ELECTRON DENSITY THAT IS DIFFICULT TO MODEL. 6. THERE IS UNMODELED ELECTRON DENSITY NEAR AMINO ACIDS GLU 83, HIS 86, GLU 140 AND HIS 170 IN BOTH PROTOMERS.
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1206 5.1 %RANDOM
Rwork0.22 ---
obs0.221 23503 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.692 Å2
Baniso -1Baniso -2Baniso -3
1-3.08 Å20 Å20 Å2
2---1.74 Å20 Å2
3----1.34 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3555 0 39 74 3668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223770
X-RAY DIFFRACTIONr_bond_other_d0.0020.022381
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9445142
X-RAY DIFFRACTIONr_angle_other_deg1.00135838
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8845483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65524.465159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.43515574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.041510
X-RAY DIFFRACTIONr_chiral_restr0.090.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024243
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02759
X-RAY DIFFRACTIONr_nbd_refined0.210.2921
X-RAY DIFFRACTIONr_nbd_other0.1690.22275
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21861
X-RAY DIFFRACTIONr_nbtor_other0.0890.21572
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1510.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.217
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.24
X-RAY DIFFRACTIONr_mcbond_it0.67922587
X-RAY DIFFRACTIONr_mcbond_other0.262953
X-RAY DIFFRACTIONr_mcangle_it1.00133802
X-RAY DIFFRACTIONr_scbond_it0.721566
X-RAY DIFFRACTIONr_scangle_it1.02831335
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1166TIGHT POSITIONAL0.030.05
1316MEDIUM POSITIONAL0.140.5
445LOOSE POSITIONAL0.725
1166TIGHT THERMAL0.10.5
1316MEDIUM THERMAL0.412
445LOOSE THERMAL1.5210
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 86 -
Rwork0.276 1583 -
all-1669 -
obs--96.87 %
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)
12.9290.25391.7382.60170.80978.25290.0797-1.0379-0.34450.17910.04510.45341.0321-1.7508-0.1248-0.2774-0.17770.00760.31430.1689-0.172-11.451924.3746-55.1856
22.0207-0.5264-0.44995.06760.5922.2690.02190.1188-0.2459-1.0114-0.01150.43330.2203-0.2351-0.0105-0.0015-0.1504-0.1451-0.33420.0369-0.2201-8.174521.0874-93.4003
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2333 - 234
2X-RAY DIFFRACTION2BB2 - 2323 - 233

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