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4cmn

Crystal structure of OCRL in complex with a phosphate ion

Method: X-RAY DIFFRACTION Dmax: 90.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

INOSITOL POLYPHOSPHATE 5-PHOSPHATASE OCRL-1

HOMO SAPIENS

UniProt Q01968

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 215–560 Fragment：5-PHOSPHATASE CATALYTIC DOMAIN, RESIDUES 215-560 Mutation：YES PO4 PHOSPHATE ION × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；0.2 M ZINC ACETATE, 0.1 M NA-CACODYLATE PH 6.5, 10% ISOPROPANOL Resolution 3.13 Å R-free 0.263

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4CMN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2KIE A PH domain within OCRL bridges clathrin mediated membrane trafficking to phosphoinositide metabolis Deposited 2009-05-03 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–119（119 aa） Fragment：N-terminal residues 1-119
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.4；298 K；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein , 20 mM potassium phosphate | 90% H2O/10% D2O
Resolution not provided
2QV2 A role of the Lowe syndrome protein OCRL in early steps of the endocytic pathway Deposited 2007-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 564–901（338 aa） Fragment：ASH-RhoGAP-like tandem domains
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；100 mM Hepes, 8.5% PEG8000, 400 mM NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.288
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp Deposited 2011-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 540–678（139 aa） Fragment：unp residues 540-678
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K
Resolution 2.00 Å R-free 0.241
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp Deposited 2011-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 540–678（139 aa） Fragment：unp residues 540-678
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K
Resolution 2.00 Å R-free 0.241
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp Deposited 2011-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 540–678（139 aa） Fragment：unp residues 540-678
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K
Resolution 2.00 Å R-free 0.241
3QBT Crystal structure of OCRL1 540-678 in complex with Rab8a:GppNHp Deposited 2011-01-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 540–678（139 aa） Fragment：unp residues 540-678
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% (w/v) PEG 4000, 20% (v/v) glycerol, 0.16 M ammonium sulphate, 0.1 M sodium acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K
Resolution 2.00 Å R-free 0.241
3QIS Recognition of the F&H motif by the Lowe Syndrome protein OCRL Deposited 2011-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 536–901（366 aa） Fragment：ASH-RhoGAP (UNP residues 536-901)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.3；291 K；1.7 M ammonium sulfate, 0.1 M MES, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.30 Å R-free 0.238

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name OCRL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–347； UniProt 215–560

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4cmn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4cmn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4cmn
Deposition date deposition_date2014-01-16
Structure title titleCrystal structure of OCRL in complex with a phosphate ion
Keywords keywordsHYDROLASE, INOSITOL SIGNALLING, SGC STOCKHOLM, STRUCTURAL GENOMICS CONSORTIUM, LOWE SYNDROME, DENT DISEASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.71 Å
Radius of gyration Rg (electron density) rg_electron21.93 Å
Forward intensity I(0) i025872400.00
Molecular weight molecular_weight38483.0 kDa
Excluded volume excluded_volume47870 ų
Envelope volume envelope_volume57456 ų
Hydration-shell volume shell_volume22670 ų
Envelope diameter envelope_diameter93.2 Å
Shell Rg shell_rg28.00 Å
Envelope Rg envelope_rg23.10 Å
Shape Rg shape_rg21.89 Å
Total Rg total_rg22.79 Å
Total atoms total_atoms2708
Residues n_residues339
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax90.3 Å
Rg (real space) rg_real22.91 Å
Rg uncertainty (real space) rg_real_error0.92 Å
I(0) (real space) i0_real2.5870e+07
I(0) uncertainty (real space) i0_real_error3.7850e+05
Rg (reciprocal space) rg_reciprocal22.86 Å
I(0) (reciprocal space) i0_reciprocal25870000.0000
Solution quality estimate total_estimate0.7449
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.0 Å
Skewness Skewness skewness0.757
Kurtosis Kurtosis kurtosis0.641
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6359000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.349; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.708; Smooth: 0.923
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id4cmnA00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily10 — Endonuclease/exonuclease/phosphatase
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8. Citations (1)

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9. Files and Curves (10)