PDB-3efh: Crystal structure of human phosphoribosyl pyrophosphate synthetase 1

Basic information

• Entry: Database: PDB / ID: 3efh
• Title: Crystal structure of human phosphoribosyl pyrophosphate synthetase 1
• Components: Ribose-phosphate pyrophosphokinase 1
• Keywords: TRANSFERASE / Charcot-Marie-Tooth disease / Deafness / Disease mutation / Gout / Kinase / Magnesium / Metal-binding / Nucleotide biosynthesis / Polymorphism

Function / homology

Function:

5-Phosphoribose 1-diphosphate biosynthesis / hypoxanthine biosynthetic process / ribose phosphate diphosphokinase complex / ribonucleoside monophosphate biosynthetic process / ribose-phosphate diphosphokinase / ribose phosphate diphosphokinase activity / urate biosynthetic process / 5-phosphoribose 1-diphosphate biosynthetic process / pyrimidine nucleotide biosynthetic process / purine nucleotide biosynthetic process / purine nucleobase metabolic process / kinase activity / nervous system development / magnesium ion binding / protein homodimerization activity / ATP binding / identical protein binding / cytosol / cytoplasm

Domain/homology:

Phosphoribosyl pyrophosphate synthetase, conserved site / Phosphoribosyl pyrophosphate synthase signature. / Ribose-phosphate pyrophosphokinase, bacterial-type / Phosphoribosyl synthetase-associated domain / N-terminal domain of ribose phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase / Ribose-phosphate pyrophosphokinase, N-terminal domain / N-terminal domain of ribose phosphate pyrophosphokinase / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta

Component:

Ribose-phosphate pyrophosphokinase 1

• Biological species: Homo sapiens (human)
• Method: X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
• Authors: Li, X. / Peng, X. / Li, Y.
• Citation: Journal: To be Published; Title: Crystal structure of human phosphoribosyl pyrophosphate synthetase 1; Authors: Peng, X. / Li, X.

History

Deposition	Sep 8, 2008	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Sep 30, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2023	Group: Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: Ribose-phosphate pyrophosphokinase 1

B: Ribose-phosphate pyrophosphokinase 1

hetero molecules

Summary:

• 72.5 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	72,477	8
Polymers	71,901	2
Non-polymers	576	6
Water	1,946	108

1

A: Ribose-phosphate pyrophosphokinase 1

B: Ribose-phosphate pyrophosphokinase 1

hetero molecules

A: Ribose-phosphate pyrophosphokinase 1

B: Ribose-phosphate pyrophosphokinase 1

hetero molecules

A: Ribose-phosphate pyrophosphokinase 1

B: Ribose-phosphate pyrophosphokinase 1

hetero molecules

Summary:

• defined by author
• 217 kDa, 6 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	217,431	24
Polymers	215,702	6
Non-polymers	1,729	18
Water	108	6

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-y,x-y,z	1
crystal symmetry operation	3_555	-x+y,-x,z	1

2

A: Ribose-phosphate pyrophosphokinase 1

hetero molecules

A: Ribose-phosphate pyrophosphokinase 1

hetero molecules

A: Ribose-phosphate pyrophosphokinase 1

hetero molecules

Summary:

• defined by software
• 109 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	108,716	12
Polymers	107,851	3
Non-polymers	865	9
Water	54	3

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-y,x-y,z	1
crystal symmetry operation	3_555	-x+y,-x,z	1

Calculated values:

Buried area	3580 Å2
ΔGint	-134 kcal/mol
Surface area	40380 Å2
Method	PISA

3

B: Ribose-phosphate pyrophosphokinase 1

hetero molecules

B: Ribose-phosphate pyrophosphokinase 1

hetero molecules

B: Ribose-phosphate pyrophosphokinase 1

hetero molecules

Summary:

• defined by software
• 109 kDa, 3 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	108,716	12
Polymers	107,851	3
Non-polymers	865	9
Water	54	3

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-y,x-y,z	1
crystal symmetry operation	3_555	-x+y,-x,z	1

Calculated values:

Buried area	3630 Å2
ΔGint	-137 kcal/mol
Surface area	40230 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	169.180, 169.180, 61.840
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

Components

#1: Protein

A B Ribose-phosphate pyrophosphokinase 1 / Phosphoribosyl pyrophosphate synthetase I / PRS-I / PPRibP

Details:

Mass: 35950.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRPS1 / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P60891, ribose-phosphate diphosphokinase

#2: Chemical

A-327 A-328 A-329 B-327 B-328 B-329
ChemComp-SO4 / SULFATE ION

Details:

Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄

#3: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H₂O

Experimental details

Experiment

• Experiment: Method: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

• Crystal: Density Matthews: 2.44 ų/Da / Density % sol: 49.62 %
• Crystal grow: Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.3 ; Details: 2.1M ammonium sulfate, 0.1M sodium acetate, 10% (v/v) glycerol, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54179 Å
• Detector: Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 18, 2005
• Radiation: Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.54179 Å / Relative weight: 1
• Reflection: Resolution: 2.6→42.295 Å / Num. all: 18873 / Num. obs: 18518 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.4 % / B_iso Wilson estimate: 50.4 Ų / R_merge(I) obs: 0.065 / R_sym value: 0.065 / Net I/σ(I): 8.5
• Reflection shell: Resolution: 2.6→2.74 Å / Redundancy: 1.4 % / R_merge(I) obs: 0.345 / Mean I/σ(I) obs: 1.8 / Num. unique all: 2623 / R_sym value: 0.345 / % possible all: 88.5

Processing

Software

Name	Version	Classification
MAR345dtb		data collection
AMoRE		phasing
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HCR

2hcr

Resolution: 2.6→30 Å / Cor.coef. F_o:F_c: 0.916 / Cor.coef. F_o:F_c free: 0.91 / SU B: 8.566 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.23133	947	5.1 %	RANDOM
Rwork	0.2157	-	-	-
all	0.21649	18508	-	-
obs	0.21649	17561	91.19 %	-

• Solvent computation: Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 33.116 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	0.79 Å2	0.39 Å2	0 Å2
2-	-	0.79 Å2	0 Å2
3-	-	-	-1.18 Å2

Refinement step

Cycle: LAST / Resolution: 2.6→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4592	0	30	108	4730

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	4680
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.08	1.957	6352
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.119	5	610
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.551	24.632	190
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.781	15	790
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.884	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	764
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	3442
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	2203
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.304	0.2	3169
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.164	0.2	247
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.221	0.2	88
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.218	0.2	14
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.49	1.5	3146
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.649	2	4902
X-RAY DIFFRACTION	r_scbond_it	0.826	3	1703
X-RAY DIFFRACTION	r_scangle_it	1.243	4.5	1450
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.6→2.667 Å / Total num. of bins used: 20

	Rfactor	Num. reflection	% reflection
Rfree	0.326	60	-
Rwork	0.302	1265	-
obs	-	-	88.04 %