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- PDB-1h97: Trematode hemoglobin from Paramphistomum epiclitum -

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Basic information

Entry
Database: PDB / ID: 1h97
TitleTrematode hemoglobin from Paramphistomum epiclitum
ComponentsGlobin-3
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / iron ion binding / heme binding
Similarity search - Function
Globin, trematode / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Globin-3
Similarity search - Component
Biological speciesParamphistomum epiclitum (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.17 Å
AuthorsPesce, A. / Dewilde, S. / Kiger, L. / Milani, M. / Ascenzi, P. / Marden, M.C. / Van Hauwaert, M.L. / Vanfleteren, J. / Moens, L. / Bolognesi, M.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Very High Resolution Structure of a Trematode Hemoglobin Displaying a Tyrb10-Tyre7 Heme Distal Residue Pair and High Oxygen Affinity
Authors: Pesce, A. / Dewilde, S. / Kiger, L. / Milani, M. / Ascenzi, P. / Marden, M.C. / Van, M.L. / Vanfleteren, J. / Moens, L. / Bolognesi, M.
History
DepositionMar 2, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2001Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 4, 2013Group: Source and taxonomy
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 23, 2019Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_database_status / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.5May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_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: Globin-3
B: Globin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8998
Polymers33,2822
Non-polymers1,6176
Water6,503361
1
A: Globin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3543
Polymers16,6411
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Globin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5465
Polymers16,6411
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.700, 83.700, 94.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9969, 0.06148, -0.0491), (0.05571, -0.11091, 0.99227), (0.05556, -0.99193, -0.11399)
Vector: 8.61937, 18.82644, 22.54264)

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Components

#1: Protein Globin-3 / Myoglobin


Mass: 16641.053 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramphistomum epiclitum (invertebrata)
Cellular location: CYTOPLASM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P80721
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 48 %
Crystal growpH: 4.5 / Details: AMMONIUM SULFATE, PH 4.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
375 %satammonium sulfate1reservoir
450 mMsodium acetate1reservoir
2potassium ferricyanide1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 1.0, 1.74
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1999 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.741
ReflectionResolution: 1.17→20 Å / Num. obs: 106124 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 17
Reflection shellResolution: 1.17→1.19 Å / Redundancy: 2 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 3 / Rsym value: 0.343 / % possible all: 84
Reflection shell
*PLUS
% possible obs: 84.2 %

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.17→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.173 5650 10 %RANDOM
obs0.121 -91.5 %-
all-56502 --
Refine analyzeNum. disordered residues: 12
Refinement stepCycle: LAST / Resolution: 1.17→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 106 361 2797
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.121
Solvent computation
*PLUS
Displacement parameters
*PLUS

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