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- PDB-1i4z: THE CRYSTAL STRUCTURE OF PHASCOLOPSIS GOULDII L98Y METHEMERYTHRIN -

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Basic information

Entry
Database: PDB / ID: 1i4z
TitleTHE CRYSTAL STRUCTURE OF PHASCOLOPSIS GOULDII L98Y METHEMERYTHRIN
ComponentsMETHEMERYTHRIN
KeywordsOXYGEN STORAGE/TRANSPORT / hemerythrin / oxygen binding / diiron / mutation / four-helix bundle / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


inorganic ion homeostasis / oxygen carrier activity / iron ion binding
Similarity search - Function
Haemerythrin / Hemerythrin-like / Hemerythrin, metal-binding domain / Haemerythrin, iron-binding site / Hemerythrin-like superfamily / Hemerythrin family signature. / Hemerythrin-like / Hemerythrin HHE cation binding domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
MU-OXO-DIIRON / Hemerythrin
Similarity search - Component
Biological speciesPhascolopsis gouldii (peanut worm)
MethodX-RAY DIFFRACTION / Difference Fourier Analysis / Resolution: 2.1 Å
AuthorsFarmer, C.S. / Kurtz Jr., D.M. / Liu, Z.-J. / Wang, B.C. / Rose, J.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2001
Title: The crystal structures of Phascolopsis gouldii wild type and L98Y methemerythrins: structural and functional alterations of the O2 binding pocket.
Authors: Farmer, C.S. / Kurtz Jr., D.M. / Liu, Z.J. / Wang, B.C. / Rose, J. / Ai, J. / Sanders-Loehr, J.
History
DepositionFeb 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 25, 2012Group: Other
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: METHEMERYTHRIN
B: METHEMERYTHRIN
C: METHEMERYTHRIN
D: METHEMERYTHRIN
E: METHEMERYTHRIN
F: METHEMERYTHRIN
G: METHEMERYTHRIN
H: METHEMERYTHRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,43316
Polymers109,4118
Non-polymers1,0228
Water7,692427
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.083, 129.991, 71.413
Angle α, β, γ (deg.)90.00, 111.22, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
METHEMERYTHRIN / HEMERYTHRIN


Mass: 13676.402 Da / Num. of mol.: 8 / Mutation: L98Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phascolopsis gouldii (peanut worm) / Production host: Escherichia coli (E. coli) / References: UniProt: P02244
#2: Chemical
ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, glycerol, HEPES, sodium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mgHr/mLprotein1drop
220 %(w/v)PEG40001reservoir
325 %(w/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 8, 1998 / Details: Yale Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→66.57 Å / Num. all: 48271 / Num. obs: 45724 / % possible obs: 85.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1 / Redundancy: 1.43 % / Biso Wilson estimate: 1.9 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 4.18
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.28 / Num. unique all: 5970 / % possible all: 67.2

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: Difference Fourier Analysis
Starting model: Phascolopsis gouldii wild type methemerythrin

Resolution: 2.1→66.57 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 25434.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.311 3703 8.1 %RANDOM
Rwork0.248 ---
all-48271 --
obs-45725 85.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.5315 Å2 / ksol: 0.424229 e/Å3
Displacement parametersBiso mean: 15 Å2
Baniso -1Baniso -2Baniso -3
1-4.87 Å20 Å20.24 Å2
2---5.67 Å20 Å2
3---0.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.1→66.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7564 0 24 427 8015
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.081.5
X-RAY DIFFRACTIONc_mcangle_it2.962
X-RAY DIFFRACTIONc_scbond_it2.862
X-RAY DIFFRACTIONc_scangle_it3.612.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.414 497 8.3 %
Rwork0.325 5474 -
obs--67.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FEO.PARFEO.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 8.1 % / Rfactor obs: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.24
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.414 / % reflection Rfree: 8.3 % / Rfactor Rwork: 0.325

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