SAXSdb — 1chm

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

CREATINE AMIDINOHYDROLASE

Pseudomonas putida

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–402 Chain B； UniProt 2–402	Not recorded	CMS CARBAMOYL SARCOSINE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CREA_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–401； UniProt 2–402 Author chain B； PDBConstruct 1–401； UniProt 2–402

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1chm
Deposition date deposition_date	1993-07-19
Structure title title	ENZYMATIC MECHANISM OF CREATINE AMIDINOHYDROLASE AS DEDUCED FROM CRYSTAL STRUCTURES
Keywords keywords	CREATINASE; CREATINASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	26.84 Å
Radius of gyration Rg (electron density) rg_electron	25.79 Å
Forward intensity I(0) i0	138343000.00
Molecular weight molecular_weight	90791.0 kDa
Excluded volume excluded_volume	112630 Å³
Envelope volume envelope_volume	128710 Å³
Hydration-shell volume shell_volume	39510 Å³
Envelope diameter envelope_diameter	89.9 Å
Shell Rg shell_rg	34.95 Å
Envelope Rg envelope_rg	25.94 Å
Shape Rg shape_rg	25.76 Å
Total Rg total_rg	26.71 Å
Total atoms total_atoms	6392
Residues n_residues	802
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	82.4 Å
Rg (real space) rg_real	26.65 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	1.3830e+08
I(0) uncertainty (real space) i0_real_error	1.7630e+06
Rg (reciprocal space) rg_reciprocal	26.71 Å
I(0) (reciprocal space) i0_reciprocal	138300000.0000
Solution quality estimate total_estimate	0.8987
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.9 Å
Skewness Skewness skewness	0.137
Kurtosis Kurtosis kurtosis	-0.444
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	139600000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.967

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CREATINE AMIDINOHYDROLASE
Molecular weight formula_weight	45333.1 kDa
EC 编号 ec_number	3.5.3.3
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6786

QMPKTLRIRNGDKVRSTFSAQEYANRQARLRAHLAAENIDAAIFTSYHNINYYSDFLYCSFGRPYALVVTEDDVISISANIDGGQPWRRTVGTDNIVYTDWQRDNYFAAIQQALPKARRIGIEHDHLNLQNRDKLAARYPDAELVDVAAACMRMRMIKSAEEHVMIRHGARIADIGGAAVVEALGDQVPEYEVALHATQAMVRAIADTFEDVELMDTWTWFQSGINTDGAHNPVTTRKVNKGDILSLNCFPMIAGYYTALERTLFLDHCSDDHLRLWQVNVEVHEAGLKLIKPGARCSDIARELNEIFLKHDVLQYRTFGYGHSFGTLSHYYGREAGLELREDIDTVLEPGMVVSMEPMIMLPEGLPGAGGYREHDILIVNENGAENITKFPYGPEKNIIR

来源 Source

来源生物 organism	Pseudomonas putida
NCBI Class编号 ncbi_taxonomy_id	303

Entity 2 Entity 2 non-polymer

Description description	CARBAMOYL SARCOSINE
Molecular weight formula_weight	132.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	394

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1chma1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.2 — Creatinase/prolidase N-terminal domain
Family Family family	c.55.2.1 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	d1chma2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.127 — Creatinase/aminopeptidase
Superfamily Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
Family Family family	d.127.1.1 — Creatinase/aminopeptidase

Domain ID domain_id	d1chmb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.2 — Creatinase/prolidase N-terminal domain
Family Family family	c.55.2.1 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	d1chmb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.127 — Creatinase/aminopeptidase
Superfamily Superfamily superfamily	d.127.1 — Creatinase/aminopeptidase
Family Family family	d.127.1.1 — Creatinase/aminopeptidase

CATH v4.4 (4 domains)

Domain ID domain_id	1chmA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	350 — Creatine Amidinohydrolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	1chmA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

Domain ID domain_id	1chmB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	350 — Creatine Amidinohydrolase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Creatinase/prolidase N-terminal domain

Domain ID domain_id	1chmB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	230 — Creatine Amidinohydrolase
Homologous superfamily homologous superfamily	10 — Creatinase/methionine aminopeptidase superfamily

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8. Citations (2)

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Unit-cell length a length_a	60.830 Å
Unit-cell length b length_b	110.550 Å
Unit-cell length c length_c	62.630 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.22 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.1770
R_free r_free	—

fit	/app/data/saxs_computation/ch/1chm/1chm.fit
pddf	/app/data/pr_computation/ch/1chm/1chm.pr.out
profile	/app/data/saxs_computation/ch/1chm/1chm.dat

ENZYMATIC MECHANISM OF CREATINE AMIDINOHYDROLASE AS DEDUCED FROM CRYSTAL STRUCTURES

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

CREATINE AMIDINOHYDROLASE

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