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- PDB-2olp: Structure and ligand selection of hemoglobin II from Lucina pectinata -

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Basic information

Entry
Database: PDB / ID: 2olp
TitleStructure and ligand selection of hemoglobin II from Lucina pectinata
ComponentsHemoglobin II
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN TRANSPORT / HEMOPROTEIN / GLOBINS / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin-2 / Hemoglobin II
Similarity search - Component
Biological speciesLucina pectinata (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.932 Å
AuthorsGavira, J.A. / Camara-Artigas, A. / de Jesus, W. / Lopez-Garriga, J. / Garcia-Ruiz, J.M.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Structure and Ligand Selection of Hemoglobin II from Lucina pectinata
Authors: Gavira, J.A. / Camara-Artigas, A. / De Jesus-Bonilla, W. / Lopez-Garriga, J. / Lewis, A. / Pietri, R. / Yeh, S.R. / Cadilla, C.L. / Garcia-Ruiz, J.M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Capillary crystallization and molecular replacement solution of Hemoglobin II of the Clam Lucina pectinata
Authors: Gavira, J.A. / de Jesus, W. / Camara-Artigas, A. / Lopez-Garriga, J. / Garcia-Ruiz, J.M.
History
DepositionJan 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Refinement description
Category: exptl_crystal_grow / pdbx_struct_special_symmetry ...exptl_crystal_grow / pdbx_struct_special_symmetry / software / struct_conn
Item: _exptl_crystal_grow.method / _software.classification ..._exptl_crystal_grow.method / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Aug 30, 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 / pdbx_initial_refinement_model / struct_conn / 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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: Author used stride method from iMoltalk.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin II
B: Hemoglobin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5728
Polymers34,0832
Non-polymers1,4896
Water4,468248
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.918, 73.918, 152.355
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-200-

SO4

21A-200-

SO4

31A-628-

HOH

41A-629-

HOH

51B-611-

HOH

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Components

#1: Protein Hemoglobin II


Mass: 17041.557 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lucina pectinata (invertebrata) / References: UniProt: Q86G74, UniProt: P41261*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 298 K / Method: counter-diffusion / pH: 7
Details: Reactor: 0.2 mm inner diameter capillary with a three layer configuration (6 microL/ 3 microL/ 30 microL). Protein chamber: 30 mg/ml in 50 mM BIS-TRIS propane pH 7.0, 0.5 mM EDTA, agarose 0. ...Details: Reactor: 0.2 mm inner diameter capillary with a three layer configuration (6 microL/ 3 microL/ 30 microL). Protein chamber: 30 mg/ml in 50 mM BIS-TRIS propane pH 7.0, 0.5 mM EDTA, agarose 0.08% (w/v). Precipitant chamber: Ammonium sulphate 2.0 M., Counter-diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97749 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97749 Å / Relative weight: 1
ReflectionResolution: 1.93→20 Å / Num. obs: 32364 / % possible obs: 99.6 % / Redundancy: 10.5 % / Biso Wilson estimate: 27.64 Å2 / Rmerge(I) obs: 0.05 / Χ2: 0.933 / Net I/σ(I): 28.81
Reflection shellResolution: 1.93→1.96 Å / % possible obs: 94 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 7 / Num. measured obs: 1704 / Num. unique all: 1587 / Χ2: 1.054 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.2.0019refinement
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACT1.7data extraction
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EBT

1ebt


Resolution: 1.932→19.838 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.165 / SU B: 4.328 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.114 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1932 1643 5.084 %RANDOM
Rwork0.165 ---
all0.166 ---
obs-32318 99.593 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.038 Å20 Å20 Å2
2--0.038 Å20 Å2
3----0.076 Å2
Refinement stepCycle: LAST / Resolution: 1.932→19.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2381 0 100 248 2729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222595
X-RAY DIFFRACTIONr_angle_refined_deg1.8412.0513533
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3225314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75624.397116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.3315446
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1291511
X-RAY DIFFRACTIONr_chiral_restr0.2470.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021959
X-RAY DIFFRACTIONr_nbd_refined0.2220.21329
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21789
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2195
X-RAY DIFFRACTIONr_metal_ion_refined0.2760.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.230
X-RAY DIFFRACTIONr_mcbond_it2.14921565
X-RAY DIFFRACTIONr_mcangle_it2.64132440
X-RAY DIFFRACTIONr_scbond_it2.34321188
X-RAY DIFFRACTIONr_scangle_it3.02331082
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
1.932-1.9820.2251370.17521580.178232398.795
1.982-2.0360.2311180.1621580.1642276100
2.036-2.0940.2431300.15920840.1642214100
2.094-2.1580.187960.1520470.1512143100
2.158-2.2280.1481280.14819880.1482116100
2.228-2.3050.2820.14619430.1482025100
2.305-2.3910.2421000.15518690.161969100
2.391-2.4870.178890.15317920.154188299.947
2.487-2.5960.19940.15917150.1611809100
2.596-2.720.191820.16216710.1631753100
2.72-2.8640.218870.16115750.1641662100
2.864-3.0340.222830.16515090.1681592100
3.034-3.2380.169740.16814310.1681505100
3.238-3.490.164750.15113330.1511408100
3.49-3.8110.153540.15612400.1561294100
3.811-4.2410.165630.14611410.147120599.917
4.241-4.8610.122640.1569950.154106299.718
4.861-5.8660.189340.2089010.20893899.68
5.866-7.9550.374320.2317120.23775398.805
7.955-19.8380.374210.2284130.23452183.301
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)
12.1784-1.03610.17015.8217-3.68044.34820.2090.215-0.03990.0006-0.26810.05940.00450.22530.0591-0.0866-0.0158-0.0272-0.2055-0.026-0.1621-4.657-5.88342.535
213.6482.79193.05522.6224-0.9482.98030.18640.32390.633-0.3749-0.31980.3026-0.27780.05880.13340.04730.0605-0.0224-0.19850.0095-0.049-15.187.28735.653
314.55861.921.830512.44454.8432.42420.22360.9563-0.0337-0.24430.02470.14640.03580.3159-0.24830.02370.0778-0.1044-0.15090.0107-0.0317-26.1832.18834.525
44.98351.46370.926911.30655.4276.2588-0.15860.0189-0.0822-0.05690.06870.83570.0158-0.06950.0898-0.07070.0098-0.0418-0.1660.0501-0.0046-29.2269.87541.547
519.95541.21091.531311.3684-4.435611.36250.52110.5042-1.0909-0.9364-0.08150.23371.2391-0.0471-0.43970.09880.0082-0.1357-0.25850.0019-0.0532-26.28315.50132.895
65.0552-6.62693.904811.6587-6.29513.54350.17810.2542-0.052-0.2521-0.14190.2347-0.00940.1856-0.0363-0.0561-0.0174-0.006-0.2246-0.0218-0.1312-12.4976.45944.698
710.363-4.39241.91333.5366-1.95775.3950.1801-0.1972-0.37930.03980.00890.18260.2266-0.1087-0.189-0.0576-0.03190.0028-0.22740.0131-0.1321-12.119-3.18757.158
87.06910.80365.46714.6465-0.83647.6052-0.01-0.148-0.00670.05410.16690.5656-0.0227-0.2581-0.1569-0.0582-0.0120.0306-0.11650.0283-0.0521-24.3873.49253.518
96.783-1.0075-6.202615.09264.752217.5401-0.08810.3754-0.30160.784-0.02370.34590.6982-1.01210.11180.012-0.0442-0.0707-0.15160.05510.0248-24.255-4.91344.822
1011.9421-1.7139-4.5256.0619-0.53878.0170.19140.6079-0.3166-0.5433-0.12340.2260.12150.2039-0.0680.05670.0551-0.0986-0.1394-0.0451-0.0852-13.502-3.28832.906
117.0151-0.7072-6.00913.29131.433415.65010.25110.20210.0884-0.3102-0.09760.11760.003-0.2646-0.1535-0.07510.0011-0.0776-0.2591-0.0151-0.0611-11.857-9.90642.307
1219.6397-9.3102-12.8426.14546.955811.9858-0.4311-0.3188-0.60160.32630.32460.84960.3385-0.28120.10650.0416-0.06930.0378-0.06030.05710.0872-23.166-6.35856.172
135.5717-2.97581.965223.1463-6.31695.22680.23170.29060.7935-0.8912-0.258-0.924-0.2667-0.3570.02620.17850.02290.1902-0.22450.02230.2278-2.0929.55347.603
143.252-1.7954-0.35993.57320.60164.90820.0988-0.24780.20150.17210.0511-0.0609-0.09730.0575-0.1499-0.0772-0.03390.0218-0.2355-0.0315-0.0957-0.45614.12358.686
155.55323.2007-0.82057.41153.06257.11450.0079-0.48550.06560.26420.05380.2171-0.1994-0.1798-0.06170.11350.08870.0672-0.02790.0507-0.1358-14.56113.55570.678
164.9265-0.6743-4.955515.1752-5.677718.49120.0632-0.4930.16751.89770.2776-0.0245-0.99050.2164-0.34090.3042-0.0681-0.0106-0.03660.0376-0.095-9.2882.7370.967
1710.8963-4.3079-0.563819.7727-3.905130.21860.0558-0.44980.04920.54070.12440.140.36430.0021-0.1802-0.0598-0.06040.0025-0.18190.0027-0.1503-8.9552.98463.248
182.89511.8318-1.97817.9147-6.1356.81990.0366-0.02260.29660.04830.06830.0579-0.1644-0.127-0.1049-0.0661-0.00410.0048-0.2298-0.0254-0.1319-8.01614.32252.651
195.66032.9093-1.94317.6556-3.31698.06430.0928-0.02560.0526-0.0202-0.074-0.1637-0.3435-0.0786-0.0188-0.03890.0291-0.0047-0.25180.0069-0.1013-15.14520.95846.032
209.127-3.40742.023713.97842.311713.4231-0.1677-0.2387-0.18510.50160.32570.648-0.0156-0.5192-0.1579-0.06570.04280.0617-0.07810.0383-0.0584-23.03215.56558.73
2116.2556-3.17121.42194.60341.25623.42430.0087-0.81620.8273-0.00190.15690.0828-0.7188-0.371-0.16560.19520.01420.0654-0.1196-0.0346-0.0717-10.56223.2663.773
2220.3442-4.16098.929724.2904-8.074338.89120.1102-0.56060.55130.80110.2516-0.8394-0.34170.3233-0.36180.1766-0.1043-0.0126-0.0173-0.15970.19223.83721.19963.062
2323.87691.0131.55739.00680.61124.4545-0.0191-0.4110.64730.03250.0049-0.7448-0.44730.0250.01420.1177-0.00110.0597-0.2204-0.0538-0.0156-5.89428.34255.372
2426.443721.944.850920.82173.77519.27980.13250.02260.4781-0.1933-0.13030.983-0.6048-0.2105-0.00220.07610.10690.04090.0132-0.01790.0772-24.31725.05154.516
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 202 - 21
22AA21 - 3122 - 32
33AA32 - 3833 - 39
44AA39 - 4940 - 50
55AA50 - 5651 - 57
66AA57 - 8258 - 83
77AA83 - 9184 - 92
88AA92 - 10293 - 103
99AA103 - 111104 - 112
1010AA112 - 124113 - 125
1111AA125 - 139126 - 140
1212AA140 - 149141 - 150
1313BB1 - 112 - 12
1414BB12 - 3113 - 32
1515BB32 - 4733 - 48
1616BB48 - 6049 - 61
1717BB61 - 6462 - 65
1818BB65 - 8066 - 81
1919BB81 - 9382 - 94
2020BB94 - 10295 - 103
2121BB103 - 118104 - 119
2222BB119 - 124120 - 125
2323BB125 - 142126 - 143
2424BB143 - 149144 - 150

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