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- PDB-4sdh: HIGH RESOLUTION CRYSTALLOGRAPHIC ANALYSIS OF A COOPERATIVE DIMERI... -

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Basic information

Entry
Database: PDB / ID: 4sdh
TitleHIGH RESOLUTION CRYSTALLOGRAPHIC ANALYSIS OF A COOPERATIVE DIMERIC HEMOGLOBIN
ComponentsHEMOGLOBIN I (DEOXY)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding / identical protein binding / cytoplasm
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-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / Resolution: 1.6 Å
AuthorsRoyerjunior, W.E.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: High-resolution crystallographic analysis of a co-operative dimeric hemoglobin.
Authors: Royer Jr., W.E.
#1: Journal: Science / Year: 1990
Title: Structural Transitions Upon Ligand Binding in a Cooperative Dimeric Hemoglobin
Authors: Royer Junior, W.E. / Hendrickson, W.A. / Chiancone, E.
#2: Journal: J.Biol.Chem. / Year: 1989
Title: The 2.4 Angstroms Crystal Structure of Scapharca Dimeric Hemoglobin. Cooperatively Based on Directly Communicating Hemes at a Novel Subunit Interface
Authors: Royer Junior, W.E. / Hendrickson, W.A. / Chiancone, E.
History
DepositionJun 23, 1993Processing site: BNL
SupersessionOct 15, 1993ID: 2SDH
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 28, 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

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN I (DEOXY)
B: HEMOGLOBIN I (DEOXY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1664
Polymers31,9332
Non-polymers1,2332
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-46 kcal/mol
Surface area12290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.880, 44.370, 143.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.3511, -0.3203, -0.8798), (-0.3096, -0.8471, 0.432), (-0.8837, 0.424, 0.1982)
Vector: 31.19, 12.99, 18.27)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*.

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Components

#1: Protein HEMOGLOBIN I (DEOXY)


Mass: 15966.319 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / References: UniProt: P02213
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal grow
*PLUS
pH: 8.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
119-22 mg/mlhemoglobin11
21.9-2.2 Mphosphate11

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 36050 / % possible obs: 96.2 % / Observed criterion σ(I): 1 / Num. measured all: 116857 / Rmerge(I) obs: 0.0832

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.158 / Rfactor obs: 0.158 / Highest resolution: 1.6 Å
Refinement stepCycle: LAST / Highest resolution: 1.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2319 0 86 219 2624
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection obs: 27830 / σ(I): 4 / Highest resolution: 1.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.030.033
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_planar_d0.050.05
X-RAY DIFFRACTIONx_plane_restr0.020.014
X-RAY DIFFRACTIONx_chiral_restr0.150.13
X-RAY DIFFRACTIONx_mcbond_it10.85
X-RAY DIFFRACTIONx_scbond_it1.51.918
X-RAY DIFFRACTIONx_mcangle_it1.51.244
X-RAY DIFFRACTIONx_scangle_it22.986

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