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- PDB-9pgx: Crystal structure of STEAP2 N-domain soaked with NADP+ -

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Basic information

Entry
Database: PDB / ID: 9pgx
TitleCrystal structure of STEAP2 N-domain soaked with NADP+
ComponentsMetalloreductase STEAP2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


copper ion import across plasma membrane / Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor / ferric-chelate reductase (NADPH) activity / iron ion import across plasma membrane / cupric reductase (NADH) activity / copper ion import / regulated exocytosis / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / response to hormone ...copper ion import across plasma membrane / Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor / ferric-chelate reductase (NADPH) activity / iron ion import across plasma membrane / cupric reductase (NADH) activity / copper ion import / regulated exocytosis / trans-Golgi network transport vesicle / Golgi to plasma membrane transport / response to hormone / endocytosis / early endosome / endosome membrane / endosome / Golgi membrane / metal ion binding / plasma membrane / cytosol
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 domain superfamily
Similarity search - Domain/homology
Chem-NDP / Metalloreductase STEAP2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsShin, I. / Liu, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA247379 United States
CitationJournal: To Be Published
Title: Crystal Structure of STEAP2 N-Domain with Its Bound NADPH Redox State Validated by Single-Crystal Spectroscopy
Authors: Shin, I. / Liu, A.
History
DepositionJul 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metalloreductase STEAP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5208
Polymers20,2661
Non-polymers1,2547
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.104, 68.104, 95.201
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-508-

HOH

21A-548-

HOH

31A-610-

HOH

41A-665-

HOH

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Components

#1: Protein Metalloreductase STEAP2 / Prostate cancer-associated protein 1 / Protein up-regulated in metastatic prostate cancer / PUMPCn ...Prostate cancer-associated protein 1 / Protein up-regulated in metastatic prostate cancer / PUMPCn / Six-transmembrane epithelial antigen of prostate 2 / SixTransMembrane protein of prostate 1


Mass: 20266.256 Da / Num. of mol.: 1 / Mutation: F65S, F69S, W102S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STEAP2, PCANAP1, STAMP1, UNQ6507/PRO23203 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8NFT2, Oxidoreductases; Oxidizing metal ions; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.14 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Bis-Tris pH 5.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 44810 / % possible obs: 99.5 % / Redundancy: 9.9 % / Biso Wilson estimate: 20.36 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.02 / Rrim(I) all: 0.064 / Χ2: 1.066 / Net I/σ(I): 9 / Num. measured all: 443112
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.46-1.499.61.18521810.7210.9160.3931.250.58197.6
1.49-1.51101.0121920.7690.9320.3281.0620.59898.3
1.51-1.5410.10.83921900.8140.9470.270.8820.60899.5
1.54-1.5710.20.63722020.890.970.2040.6690.63599.5
1.57-1.6110.20.58322150.9120.9770.1880.6130.61699.5
1.61-1.64100.49322210.9350.9830.160.5190.65499.4
1.64-1.699.90.42322230.9550.9880.1390.4450.67899.6
1.69-1.739.60.33922100.9660.9910.1130.3580.73599.7
1.73-1.788.80.25822130.9720.9930.0910.2740.80299.5
1.78-1.849.80.20722450.9820.9950.0680.2180.83999.8
1.84-1.9110.40.17522130.9910.9980.0560.1840.97499.8
1.91-1.9810.30.14422520.9920.9980.0460.1511.10399.9
1.98-2.0710.20.12822300.9940.9980.0410.1341.391100
2.07-2.18100.09922420.9960.9990.0320.1041.479100
2.18-2.329.80.08422450.9970.9990.0280.0891.639100
2.32-2.590.07322580.9960.9990.0260.0771.76699.3
2.5-2.75100.06222630.9980.9990.020.0651.88699.8
2.75-3.1510.50.05322910.99810.0170.0561.869100
3.15-3.9610.10.03823160.99910.0120.041.626100
3.96-509.30.0232408110.0080.0240.72398.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data scaling
DENZOdata reduction
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46→29.49 Å / SU ML: 0.133 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.3989
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1832 1993 4.45 %
Rwork0.1587 42761 -
obs0.1598 44754 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.78 Å2
Refinement stepCycle: LAST / Resolution: 1.46→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1401 0 76 207 1684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00691530
X-RAY DIFFRACTIONf_angle_d1.16582095
X-RAY DIFFRACTIONf_chiral_restr0.0876243
X-RAY DIFFRACTIONf_plane_restr0.0064260
X-RAY DIFFRACTIONf_dihedral_angle_d8.6536219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.50.23651410.21122964X-RAY DIFFRACTION97.64
1.5-1.540.22581410.17962985X-RAY DIFFRACTION98.86
1.54-1.580.24171390.18243042X-RAY DIFFRACTION99.53
1.58-1.630.21831370.16483001X-RAY DIFFRACTION99.37
1.63-1.690.17931370.16233017X-RAY DIFFRACTION99.56
1.69-1.760.19661460.14393023X-RAY DIFFRACTION99.53
1.76-1.840.17481430.14483052X-RAY DIFFRACTION99.72
1.84-1.940.1841380.1413030X-RAY DIFFRACTION99.78
1.94-2.060.19391450.15263066X-RAY DIFFRACTION99.97
2.06-2.220.17211400.13263064X-RAY DIFFRACTION99.94
2.22-2.440.17651420.15763087X-RAY DIFFRACTION99.94
2.44-2.790.17381470.16633057X-RAY DIFFRACTION99.44
2.79-3.520.17241430.16653135X-RAY DIFFRACTION100
3.52-29.490.18411540.15973238X-RAY DIFFRACTION99.41

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