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- PDB-2jjz: Crystal Structure of Human Iba2, orthorhombic crystal form -

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Basic information

Entry
Database: PDB / ID: 2jjz
TitleCrystal Structure of Human Iba2, orthorhombic crystal form
Components(IONIZED CALCIUM-BINDING ADAPTER MOLECULE ...) x 2
KeywordsMETAL BINDING PROTEIN / EF-HAND / CALCIUM BINDING / ACTIN CROSSLINKING / IONIZED CALCIUM BINDING ADAPTER MOLECULE 2 / METAL-BINDING PROTEIN
Function / homology
Function and homology information


ruffle assembly / actin filament bundle assembly / ruffle membrane / actin filament binding / actin cytoskeleton / focal adhesion / calcium ion binding / extracellular exosome / cytoplasm
Similarity search - Function
Allograft inflammatory factor 1 / : / Allograft inflammatory factor 1 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
ACETATE ION / Allograft inflammatory factor 1-like
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSchulze, J.O. / Quedenau, C. / Roske, Y. / Turnbull, A. / Mueller, U. / Heinemann, U. / Buessow, K.
CitationJournal: FEBS J. / Year: 2008
Title: Structural and Functional Characterization of Human Iba Proteins.
Authors: Schulze, J.O. / Quedenau, C. / Roske, Y. / Adam, T. / Schuler, H. / Behlke, J. / Turnbull, A.P. / Sievert, V. / Scheich, C. / Mueller, U. / Heinemann, U. / Bussow, K.
History
DepositionMay 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IONIZED CALCIUM-BINDING ADAPTER MOLECULE 2
B: IONIZED CALCIUM-BINDING ADAPTER MOLECULE 2
C: IONIZED CALCIUM-BINDING ADAPTER MOLECULE 2
D: IONIZED CALCIUM-BINDING ADAPTER MOLECULE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,84513
Polymers68,3714
Non-polymers4749
Water3,999222
1
A: IONIZED CALCIUM-BINDING ADAPTER MOLECULE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2173
Polymers17,0931
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: IONIZED CALCIUM-BINDING ADAPTER MOLECULE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1943
Polymers17,0931
Non-polymers1012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: IONIZED CALCIUM-BINDING ADAPTER MOLECULE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2765
Polymers17,0931
Non-polymers1834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: IONIZED CALCIUM-BINDING ADAPTER MOLECULE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1582
Polymers17,0931
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.540, 186.500, 51.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-1130-

NA

21D-1123-

ZN

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22D
13C
23D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 5 / Auth seq-ID: 57 - 105 / Label seq-ID: 57 - 105

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21DD
12BB
22DD
13CC
23DD

NCS ensembles :
ID
1
2
3

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Components

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IONIZED CALCIUM-BINDING ADAPTER MOLECULE ... , 2 types, 4 molecules ABCD

#1: Protein IONIZED CALCIUM-BINDING ADAPTER MOLECULE 2 / IONIZED CALCIUM ADAPTER MOLECULE 2 / C9ORF58


Mass: 17092.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SCS1 / References: UniProt: Q9BQI0
#2: Protein IONIZED CALCIUM-BINDING ADAPTER MOLECULE 2 / IONIZED CALCIUM ADAPTER MOLECULE 2 / C9ORF58


Mass: 17092.838 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): SCS1 / References: UniProt: Q9BQI0

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Non-polymers , 5 types, 231 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 50.94 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI-111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 38251 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.1
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WY9

1wy9


Resolution: 2.15→19.81 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.498 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1913 5 %RANDOM
Rwork0.216 ---
obs0.218 36336 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.08 Å2
Baniso -1Baniso -2Baniso -3
1--4.54 Å20 Å20 Å2
2--1.71 Å20 Å2
3---2.84 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3401 0 15 222 3638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223451
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5882.0014589
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6935415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.46124.667165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77215750
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6611527
X-RAY DIFFRACTIONr_chiral_restr0.110.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022490
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.21517
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22357
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2209
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.262
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8261.52079
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.50323330
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.66631384
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1394.51258
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A108medium positional0.340.5
2B107medium positional0.340.5
3C108medium positional0.350.5
1A96loose positional0.575
2B92loose positional0.565
3C96loose positional0.645
1A108medium thermal0.882
2B107medium thermal1.712
3C108medium thermal1.022
1A96loose thermal1.0810
2B92loose thermal1.7710
3C96loose thermal1.2510
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.323 137
Rwork0.265 2601
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.75372.90262.90343.49983.26923.97270.0961-0.24670.05490.0689-0.26570.11520.0176-0.46220.16950.19670.0111-0.0071-0.1286-0.0669-0.166953.05663.74426.252
29.23924.12376.1314.7134.61856.00940.2794-0.2343-0.3390.2075-0.28750.11890.0842-0.36480.0080.1522-0.0062-0.0219-0.1255-0.0492-0.220453.05663.74426.252
33.32460.16252.3520.6490.10972.6834-0.0804-0.2050.080.1051-0.02440.003-0.192-0.22620.10470.13760.00790.0238-0.1379-0.0714-0.139229.64948.1223.342
44.0555-0.40511.35890.2668-0.31321.2246-0.0287-0.29060.29620.0575-0.0635-0.0096-0.1725-0.09790.09220.18180.00120.0273-0.1156-0.0516-0.089429.64948.1223.342
50.6644-0.0252-0.53852.9240.02973.39790.04030.0985-0.0582-0.2721-0.0924-0.15480.37080.2010.0520.17940.05090.0353-0.1077-0.0224-0.160840.13824.981-3.277
61.24620.68150.43214.84130.61887.3158-0.02230.1032-0.1491-0.0342-0.103-0.16450.460.31760.12530.14310.07420.0442-0.1215-0.0235-0.215640.13824.981-3.277
74.4325-4.04281.086316.5141-1.43753.7716-0.1238-0.37220.15231.7071-0.1823-1.90420.17110.23840.30620.4769-0.0236-0.1821-0.17880.08260.133243.1556.05323.784
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 79
2X-RAY DIFFRACTION2A80 - 125
3X-RAY DIFFRACTION3B16 - 79
4X-RAY DIFFRACTION4B80 - 127
5X-RAY DIFFRACTION5C13 - 79
6X-RAY DIFFRACTION6C80 - 127
7X-RAY DIFFRACTION7D20 - 122

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