PDB-2zzs: Crystal structure of cytochrome c554 from Vibrio parahaemolyticus...

Basic information

• Entry: Database: PDB / ID: 2zzs
• Title: Crystal structure of cytochrome c554 from Vibrio parahaemolyticus strain RIMD2210633
• Components: Cytochrome c554
• Keywords: ELECTRON TRANSPORT / c-type cytochrome / cytochrome c554

Function / homology

Function:

electron transfer activity / iron ion binding / heme binding

Domain/homology:

Cytochrome c, class IC / Cytochrome c / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Alpha

Component:

HEME C / Cytochrome c554

• Biological species: Vibrio parahaemolyticus (bacteria)
• Method: X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
• Authors: Akazaki, H. / Kawai, F. / Kumaki, Y. / Sekine, K. / Hakamata, W. / Nishio, T. / Park, S.-Y. / Oku, T.
• Citation: Journal: To be Published; Title: Crystal structure of cytochrome c554 from Vibrio parahaemolyticus strain RIMD2210633; Authors: Akazaki, H. / Kawai, F. / Kumaki, Y. / Sekine, K. / Hakamata, W. / Nishio, T. / Park, S.-Y. / Oku, T.

History

Deposition	Feb 24, 2009	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Mar 16, 2010	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_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Assembly

Deposited unit

A: Cytochrome c554

B: Cytochrome c554

C: Cytochrome c554

D: Cytochrome c554

E: Cytochrome c554

F: Cytochrome c554

G: Cytochrome c554

H: Cytochrome c554

I: Cytochrome c554

J: Cytochrome c554

K: Cytochrome c554

L: Cytochrome c554

M: Cytochrome c554

N: Cytochrome c554

O: Cytochrome c554

P: Cytochrome c554

Q: Cytochrome c554

R: Cytochrome c554

S: Cytochrome c554

T: Cytochrome c554

U: Cytochrome c554

V: Cytochrome c554

W: Cytochrome c554

X: Cytochrome c554

Y: Cytochrome c554

Z: Cytochrome c554

1: Cytochrome c554

2: Cytochrome c554

3: Cytochrome c554

4: Cytochrome c554

5: Cytochrome c554

6: Cytochrome c554

hetero molecules

Summary:

• 355 kDa, 32 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	355,294	68
Polymers	335,134	32
Non-polymers	20,160	36
Water	29,256	1624

1

A: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

2

B: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

3

C: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,184	3
Polymers	10,473	1
Non-polymers	711	2
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

4

D: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

5

E: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,184	3
Polymers	10,473	1
Non-polymers	711	2
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

6

F: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

7

G: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

8

H: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

9

I: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

10

J: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

11

K: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

12

L: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

13

M: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

14

N: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

15

O: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

16

P: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,184	3
Polymers	10,473	1
Non-polymers	711	2
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

17

Q: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

18

R: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.2 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,184	3
Polymers	10,473	1
Non-polymers	711	2
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

19

S: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

20

T: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

21

U: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

22

V: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

23

W: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

24

X: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

25

Y: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

26

Z: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

27

1: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

28

2: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

29

3: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

30

4: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

31

5: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

32

6: Cytochrome c554

hetero molecules

Summary:

• defined by author
• 11.1 kDa, 1 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	11,091	2
Polymers	10,473	1
Non-polymers	619	1
Water	18	1

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1

Unit cell

Length a, b, c (Å)	84.949, 87.612, 103.847
Angle α, β, γ (deg.)	71.50, 72.98, 83.68
Int Tables number	1
Space group name H-M	P1

Components

#1: Protein

A B C D E F G H I J K L M N O P Q R S ...
Cytochrome c554

Details:

Mass: 10472.924 Da / Num. of mol.: 32
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD2210633 / Gene: VP2300 / Production host: Escherichia coli (E. coli) / References: UniProt: Q87MF5

#2: Chemical

A-220 B-220 C-220 D-220 E-220 F-220 G-220 H-220 I-220 J-220 K-220 L-220 M-220 N-220 O-220 P-220 Q-220 R-220 S-220 T-220 ...
ChemComp-HEC / HEME C / Heme C

Details:

Mass: 618.503 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: C₃₄H₃₄FeN₄O₄

#3: Chemical

C-104 E-104 P-104 R-104
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol

Details:

Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃

#4: Water

ChemComp-HOH / water / Water

Details:

Mass: 18.015 Da / Num. of mol.: 1624 / 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: 2.09 ų/Da / Density % sol: 41.17 %
• Crystal grow: Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.2 ; Details: 10mM sodium phosphate buffer (pH 7.0), 0.1M phosphate-citrate (pH 4.2), 0.2M NaCl, 20%(w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Data collection

• Diffraction: Mean temperature: 100 K
• Diffraction source: Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
• Detector: Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 5, 2008
• Radiation: Monochromator: Numerical link type Si(111) double crystal monochromator; Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1 Å / Relative weight: 1
• Reflection: Resolution: 1.8→20 Å / Num. all: 235784 / Num. obs: 223962 / % possible obs: 94.5 % / R_merge(I) obs: 0.063
• Reflection shell: Resolution: 1.8→1.86 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.205 / Mean I/σ(I) obs: 14.1 / Num. unique all: 19421 / R_sym value: 0.23 / % possible all: 77.9

Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
MOLREP		phasing
REFMAC	5.4.0067	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GDV

1gdv

Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.24213	11820	-	RANDOM
Rwork	0.19269	-	-	-
obs	0.19519	223962	100 %	-
all	-	235784	-	-

Displacement parameters

B_iso mean: 26.068 Ų

	Baniso -1	Baniso -2	Baniso -3
1-	-0.26 Å2	0.48 Å2	-0.16 Å2
2-	-	-0.79 Å2	0.04 Å2
3-	-	-	1.02 Å2

Refinement step

Cycle: LAST / Resolution: 1.8→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18378	0	1400	1624	21402

Refine LS restraints

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_refined_d	0.018
X-RAY DIFFRACTION	r_angle_refined_deg	1.777
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.065
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.766
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.377
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	7.43
X-RAY DIFFRACTION	r_chiral_restr	0.111
X-RAY DIFFRACTION	r_gen_planes_refined	0.011
X-RAY DIFFRACTION	r_mcbond_it	1.001
X-RAY DIFFRACTION	r_mcangle_it	1.742
X-RAY DIFFRACTION	r_scbond_it	2.77
X-RAY DIFFRACTION	r_scangle_it	4.072

LS refinement shell

Resolution: 1.803→1.849 Å

	Rfactor	Num. reflection	% reflection
Rfree	0.295	637	-
Rwork	0.228	-	-
obs	-	-	100 %