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- PDB-4d4z: STRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE in complex with glycerol -

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Basic information

Entry
Database: PDB / ID: 4d4z
TitleSTRUCTURE OF HUMAN DEOXYHYPUSINE HYDROXYLASE in complex with glycerol
ComponentsDEOXYHYPUSINE HYDROXYLASE
KeywordsOXIDOREDUCTASE / EIF-5A / HYPUSINE
Function / homology
Function and homology information


deoxyhypusine monooxygenase / deoxyhypusine monooxygenase activity / peptidyl-hypusine biosynthetic process / Hypusine synthesis from eIF5A-lysine / iron ion binding / cytosol
Similarity search - Function
Deoxyhypusine hydroxylase / E-Z type HEAT repeats / PBS lyase HEAT-like repeat / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
: / HYDROXIDE ION / Deoxyhypusine hydroxylase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsHan, Z. / Sakai, N. / Hilgenfeld, R.
CitationJournal: Structure / Year: 2015
Title: Crystal Structure of the Peroxo-Diiron(III) Intermediate of Deoxyhypusine Hydroxylase, an Oxygenase Involved in Hypusination.
Authors: Han, Z. / Sakai, N. / Bottger, L.H. / Klinke, S. / Hauber, J. / Trautwein, A.X. / Hilgenfeld, R.
History
DepositionOct 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2May 27, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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: DEOXYHYPUSINE HYDROXYLASE
B: DEOXYHYPUSINE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,70611
Polymers63,9822
Non-polymers7249
Water6,035335
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A: DEOXYHYPUSINE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4946
Polymers31,9911
Non-polymers5035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DEOXYHYPUSINE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2125
Polymers31,9911
Non-polymers2214
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.051, 70.175, 101.275
Angle α, β, γ (deg.)90.00, 102.71, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given / Matrix: (1), (1), (1))

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DEOXYHYPUSINE HYDROXYLASE / HDOHH / DEOXYHYPUSINE DIOXYGENASE / DEOXYHYPUSINE MONOOXYGENASE / HEAT-LIKE REPEAT-CONTAINING PROTEIN 1


Mass: 31991.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9BU89, deoxyhypusine monooxygenase

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Non-polymers , 5 types, 344 molecules

#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsFIVE RESIDUES (GPLGS) IN N-TERMINUS ARE FROM EXPRESSION VECTOR

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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: 2.49 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.2
Details: 30% POLYETHYLENE GLYCOL 6000 (W/V), 100 MM BIS-TRIS PROPANE PH 7.2 - 7.4, 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.7→44.92 Å / Num. obs: 68054 / % possible obs: 98.2 % / Observed criterion σ(I): 6 / Redundancy: 4 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.5
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 6 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.7→19.95 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.649 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19283 3423 5 %RANDOM
Rwork0.17024 ---
obs0.1714 64571 98.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.665 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.06 Å2
2---0.38 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4399 0 37 335 4771
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194581
X-RAY DIFFRACTIONr_bond_other_d0.0060.024385
X-RAY DIFFRACTIONr_angle_refined_deg2.0071.9846224
X-RAY DIFFRACTIONr_angle_other_deg1.284310086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7295594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.60223.874222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84315745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5811544
X-RAY DIFFRACTIONr_chiral_restr0.1290.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0215288
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021016
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 220 -
Rwork0.198 4063 -
obs--84.8 %

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