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- PDB-1jf4: Crystal Structure Of Component IV Glycera Dibranchiata Monomeric ... -

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Basic information

Entry
Database: PDB / ID: 1jf4
TitleCrystal Structure Of Component IV Glycera Dibranchiata Monomeric Hemoglobin
Componentsmonomer hemoglobin component IV
KeywordsOXYGEN STORAGE/TRANSPORT / Glycera / monomer hemoglobin / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
: / 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, monomeric component M-IV
Similarity search - Component
Biological speciesGlycera dibranchiata (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPark, H.J. / Yang, C. / Treff, N. / Satterlee, J.D. / Kang, C.H.
CitationJournal: Proteins / Year: 2002
Title: Crystal Structures of Unligated and CN-Ligated Glycera dibranchiata Monomer Ferric Hemoglobin Components III and IV
Authors: Park, H.J. / Yang, C. / Treff, N. / Satterlee, J.D. / Kang, C.
History
DepositionJun 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: monomer hemoglobin component IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6662
Polymers15,0491
Non-polymers6161
Water1,35175
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.94, 33.00, 40.76
Angle α, β, γ (deg.)90, 109.61, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein monomer hemoglobin component IV / GMH4


Mass: 15049.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycera dibranchiata (invertebrata) / References: UniProt: P15447
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.57 Å3/Da / Density % sol: 52.05 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, sodium acetate, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
215 %PEG40001drop
350 mMsodium acetate1drop
40.1 Mammonium sulfate1droppH4.6
530 %PEG40001reservoir
6100 mMsodium acetate1reservoir
70.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 7, 2000 / Details: mirror
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 12323 / Num. obs: 11627 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.049
Reflection shellResolution: 1.4→30 Å / Redundancy: 3.5 % / % possible all: 90
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. obs: 10227 / % possible obs: 89 % / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Rmerge(I) obs: 36

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→10 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1602 14.3 %RANDOM
Rwork0.189 ---
all-11464 --
obs-11172 --
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 43 75 1174
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d2.255
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. reflection obs: 10821 / % reflection Rfree: 5 % / Rfactor obs: 0.189 / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_d2.25
LS refinement shell
*PLUS
Rfactor Rfree: 0.275 / Rfactor Rwork: 0.234 / Rfactor obs: 0.234

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