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- PDB-2yjz: Rat STEAP4 oxidoreductase domain complexed with NADP -

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Basic information

Entry
Database: PDB / ID: 2yjz
TitleRat STEAP4 oxidoreductase domain complexed with NADP
ComponentsMETALLOREDUCTASE STEAP4
KeywordsOXIDOREDUCTASE / METABOLIC SYNDROME
Function / homology
Function and homology information


iron ion import across cell outer membrane / ferric-chelate reductase (NADPH) / ferric-chelate reductase (NADPH) activity / cupric reductase (NADH) activity / : / copper ion import / : / fat cell differentiation / protein homotrimerization / FAD binding ...iron ion import across cell outer membrane / ferric-chelate reductase (NADPH) / ferric-chelate reductase (NADPH) activity / cupric reductase (NADH) activity / : / copper ion import / : / fat cell differentiation / protein homotrimerization / FAD binding / early endosome membrane / membrane => GO:0016020 / electron transfer activity / endosome / Golgi membrane / heme binding / nucleoplasm / metal ion binding / plasma membrane
Similarity search - Function
Ferric reductase transmembrane component-like domain / Ferric reductase like transmembrane component / Pyrroline-5-carboxylate reductase, catalytic, N-terminal / NADP oxidoreductase coenzyme F420-dependent / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Metalloreductase STEAP4
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGauss, G.H. / Kleven, M.D. / Sendamarai, A.K. / Fleming, M.D. / Lawrence, C.M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The Crystal Structure of Six-Transmembrane Epithelial Antigen of the Prostate 4 (Steap4), a Ferri/Cuprireductase, Suggests a Novel Interdomain Flavin-Binding Site.
Authors: Gauss, G.H. / Kleven, M.D. / Sendamarai, A.K. / Fleming, M.D. / Lawrence, C.M.
History
DepositionMay 24, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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 / _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: METALLOREDUCTASE STEAP4
B: METALLOREDUCTASE STEAP4
C: METALLOREDUCTASE STEAP4
D: METALLOREDUCTASE STEAP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,50913
Polymers88,0564
Non-polymers3,4549
Water4,035224
1
A: METALLOREDUCTASE STEAP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8533
Polymers22,0141
Non-polymers8392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: METALLOREDUCTASE STEAP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8533
Polymers22,0141
Non-polymers8392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: METALLOREDUCTASE STEAP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9494
Polymers22,0141
Non-polymers9363
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: METALLOREDUCTASE STEAP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8533
Polymers22,0141
Non-polymers8392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.228, 85.111, 128.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22C
13B
23D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 50
2111B1 - 50
3111C1 - 50
4111D1 - 50
1211A124 - 201
2211B124 - 201
3211C124 - 201
4211D124 - 201
1121A51 - 123
2121C51 - 123
1131B51 - 123
2131D51 - 123

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.96511, -0.26131, -0.01643), (-0.26006, 0.96399, -0.05571), (0.0304, -0.04949, -0.99831)96.78766, 16.01169, 118.53529
2given(0.99945, 0.01992, -0.02634), (0.01991, -0.9998, -0.00057), (-0.02635, 4.0E-5, -0.99965)1.68163, 45.69936, 129.04858
3given(-0.96902, 0.24696, 0.00288), (-0.24644, -0.96761, 0.0548), (0.01631, 0.05239, 0.99849)83.80499, 53.13784, -10.88943

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Components

#1: Protein
METALLOREDUCTASE STEAP4 / SIX-TRANSMEMBRANE EPITHELIAL ANTIGEN OF PROSTATE 4 STEAP4


Mass: 22013.891 Da / Num. of mol.: 4 / Fragment: OXIDOREDUCTASE DOMAIN, RESIDUES 1-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q4V8K1, Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.07 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1 M BIS-TRIS HCL PH 5.5; 2.1 M AMMONIUM SULFATE; 0.001M NADPH.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.99984
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 39044 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.8 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQ3

2vq3


Resolution: 2.2→37 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.889 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-18 AND 147-149 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.23784 1948 5 %RANDOM
Rwork0.20285 ---
obs0.20471 36854 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.747 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--2.79 Å20 Å2
3----2.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5292 0 217 224 5733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0225610
X-RAY DIFFRACTIONr_bond_other_d00.023672
X-RAY DIFFRACTIONr_angle_refined_deg1.8612.0117632
X-RAY DIFFRACTIONr_angle_other_deg3.89738980
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1035690
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.4824.576236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67415910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8731532
X-RAY DIFFRACTIONr_chiral_restr0.0990.2866
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026127
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021053
X-RAY DIFFRACTIONr_nbd_refined0.2110.21012
X-RAY DIFFRACTIONr_nbd_other0.2330.23374
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22760
X-RAY DIFFRACTIONr_nbtor_other0.1050.22745
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2264
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1260.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3120.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3680.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9851.53443
X-RAY DIFFRACTIONr_mcbond_other0.0211.51421
X-RAY DIFFRACTIONr_mcangle_it1.9125506
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.87332167
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5454.52125
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1331tight positional0.070.05
12B1331tight positional0.070.05
13C1331tight positional0.120.05
14D1331tight positional0.070.05
21A953tight positional0.110.05
22C953tight positional0.110.05
31B953tight positional0.050.05
32D953tight positional0.050.05
11A1331tight thermal0.230.5
12B1331tight thermal0.210.5
13C1331tight thermal0.210.5
14D1331tight thermal0.210.5
21A953tight thermal0.240.5
22C953tight thermal0.240.5
31B953tight thermal0.220.5
32D953tight thermal0.220.5
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 124 -
Rwork0.247 2535 -
obs--94.16 %

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