9zid

Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 5

Method: ELECTRON MICROSCOPY D_max: 162.3 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribonuclease P protein component

Geobacillus stearothermophilus

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–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 1–115	Not recorded	RNase P RNA (417-MER) × 1 MG MAGNESIUM ION × 29	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.40 Å

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 9ZID	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9OWS Structure of Geobacillus stearothermophilus RNase P holoenzyme in 5 mM Mg2+ Deposited 2025-06-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.87 Å
9OWT Structure of Geobacillus stearothermophilus RNase P holoenzyme in complex with precursor tRNA in 5 mM Ca2+ Deposited 2025-06-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 1–115（115 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.82 Å
9OWU Structure of Geobacillus stearothermophilus RNase P holoenzyme in complex with precursor tRNA in 1 mM Ca2+ Deposited 2025-06-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: tetrameric	Chain B 1–115（115 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.93 Å
9OWV Structure of Geobacillus stearothermophilus RNase P holoenzyme in complex with mature tRNA in 5 mM Ca2+ Deposited 2025-06-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–115（115 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 3.02 Å
9OWW Structure of Geobacillus stearothermophilus RNase P holoenzyme in complex with the precursor tRNA with non-complementary 5' leader Deposited 2025-06-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–115（115 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.83 Å
9OWX Structure of Geobacillus stearothermophilus RNase P holoenzyme in complex with the precursor tRNA with loop-back 5' leader (sub-conformation 1 of tRNA anticodon arm tilted) Deposited 2025-06-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–115（115 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.70 Å
9OWY Structure of Geobacillus stearothermophilus RNase P holoenzyme in complex with the precursor tRNA with loop-back 5' leader (sub-conformation 2 of tRNA anticodon arm tilted) Deposited 2025-06-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–115（115 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 2.69 Å
9ZI8 Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 1 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 34	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.18 Å
9ZI9 Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 2 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 33	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9ZIB Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 3 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 41	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9ZIC Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 4 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 24	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9ZIE Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 6 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 36	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
9ZIF Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 7 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 33	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9ZIG Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 8 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.44 Å
9ZIH Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 9 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 38	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
9ZII Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 10 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 31	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
9ZIJ Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 11 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 35	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
9ZIK Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 12 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 27	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9ZIL Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 13 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 36	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9ZIM Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 14 Deposited 2025-12-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
9ZIN Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 15 Deposited 2025-12-03	Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 29	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
9ZIU Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 16 Deposited 2025-12-04	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 35	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
9ZIV Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 17 Deposited 2025-12-04	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 38	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
9ZIW Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 18 Deposited 2025-12-04	Different ligand/ion	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 41	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9ZIX Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 20 Deposited 2025-12-04	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 24	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.68 Å
9ZIY Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 21 Deposited 2025-12-04	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 21	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9ZIZ Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 19 Deposited 2025-12-04	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–115（115 aa）	Not recorded	MG MAGNESIUM ION × 40	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å

27 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A150N245_GEOSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–116； UniProt 1–115

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9zid
Deposition date deposition_date	2025-12-03
Structure title title	Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 5
Keywords keywords	ribozyme, RNA, RNase P, RNA-HYDROLASE complex; RNA/HYDROLASE
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	47.10 Å
Radius of gyration Rg (electron density) rg_electron	47.40 Å
Forward intensity I(0) i0	934968000.00
Molecular weight molecular_weight	149920.0 kDa
Excluded volume excluded_volume	144060 Å³
Envelope volume envelope_volume	260390 Å³
Hydration-shell volume shell_volume	49849 Å³
Envelope diameter envelope_diameter	169.8 Å
Shell Rg shell_rg	46.68 Å
Envelope Rg envelope_rg	46.43 Å
Shape Rg shape_rg	47.38 Å
Total Rg total_rg	47.40 Å
Total atoms total_atoms	9938
Residues n_residues	533
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	162.3 Å
Rg (real space) rg_real	47.49 Å
Rg uncertainty (real space) rg_real_error	1.60 Å
I(0) (real space) i0_real	9.3500e+08
I(0) uncertainty (real space) i0_real_error	1.9050e+07
Rg (reciprocal space) rg_reciprocal	47.10 Å
I(0) (reciprocal space) i0_reciprocal	934500000.0000
Solution quality estimate total_estimate	0.8488
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.3 Å
Skewness Skewness skewness	0.463
Kurtosis Kurtosis kurtosis	-0.417
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	26940000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.827; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.918; Smooth: 0.632

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	RNase P RNA (417-MER)
Molecular weight formula_weight	135305.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	9939

GUUAAUCAUGCUCGGGUAAUCGCUGCGGCCGGUUUCGGCCGUAGAGGAAAGUCCAUGCUCGCACGGUGCUGAGAUGCCCGUAGUGUUCGUGCCUAGCGAAUCCAUAAGCUAGGGCAGCCUGGCUUUGGCUGGGCUGACGGCGGGGAAAGAACCUACGUCCGGCUGGGAUAUGGUUCGAUUACCCUGAAAGUGCCACAGUGACGGAGCUCUAAGGGAAACCUUAGAGGUGGAACGCGGUAAACCCCACGAGCGAGAAACCCAAAUGAUGGUAGGGGCACCUUCCCGAAGGAAAUGAACGGAGGGAAGGACAGGCGGCGCAUGCAGCCUGUAGAUAGAUGAUUACCGCCGGAGUACGAGGCGCAAAGCCGCUUGCAGUACGAAGGUACAGAACAUGGCUUAUAGAGCAUGAUUAACGUC

来源 Source

来源生物 organism	Geobacillus stearothermophilus
NCBI Class编号 ncbi_taxonomy_id	1422
宿主生物 host_organism	in vitro transcription vector pT7-TP(deltai)

Entity 2 Entity 2 polymer

Description description	Ribonuclease P protein component
Molecular weight formula_weight	13456.9 kDa
EC 编号 ec_number	3.1.26.5
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GMKKKYRIKKNEEFQEVFQQGVSVANRQFVVYTLDRPEQPYFRIGLSVSKKLGKAVVRNRIKRYIRQCFLELKEEVAPGKDYVIIARQPAAEMGYAEVKKSLIHVLRKAGGLKKEA

来源 Source

来源生物 organism	Geobacillus stearothermophilus
NCBI Class编号 ncbi_taxonomy_id	1422
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	29

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.40 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	998359

fit	/app/data/saxs_computation/zi/9zid/9zid.fit
pddf	/app/data/pr_computation/zi/9zid/9zid.pr.out
profile	/app/data/saxs_computation/zi/9zid/9zid.dat

Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 5

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribonuclease P protein component

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)