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- PDB-5k89: Crystal Structure of Human Calcium-Bound S100A1 -

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Basic information

Entry
Database: PDB / ID: 5k89
TitleCrystal Structure of Human Calcium-Bound S100A1
ComponentsProtein S100-A1
KeywordsMETAL BINDING PROTEIN / S100 / S100A1 / calcium
Function / homology
Function and homology information


Regulation of TLR by endogenous ligand / RAGE receptor binding / MyD88 deficiency (TLR2/4) / S100 protein binding / regulation of heart contraction / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of sprouting angiogenesis / substantia nigra development / sarcoplasmic reticulum ...Regulation of TLR by endogenous ligand / RAGE receptor binding / MyD88 deficiency (TLR2/4) / S100 protein binding / regulation of heart contraction / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / positive regulation of sprouting angiogenesis / substantia nigra development / sarcoplasmic reticulum / positive regulation of nitric-oxide synthase activity / calcium-dependent protein binding / ER-Phagosome pathway / ATPase binding / positive regulation of canonical NF-kappaB signal transduction / intracellular signal transduction / calcium ion binding / positive regulation of cell population proliferation / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular space / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Protein S100-A1 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif ...Protein S100-A1 / S-100/ICaBP type calcium binding protein signature. / S100/Calcium binding protein 7/8-like, conserved site / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / EF hand / EF-hand / Recoverin; domain 1 / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.249 Å
AuthorsMelville, Z. / Aligholizadeh, E. / McKnight, L.E. / Weber, D. / Pozharski, E. / Weber, D.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA-107331 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-58888 United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)AR007592 United States
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: X-ray crystal structure of human calcium-bound S100A1.
Authors: Melville, Z. / Aligholizadeh, E. / McKnight, L.E. / Weber, D.J. / Pozharski, E. / Weber, D.J.
History
DepositionMay 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_assembly ...pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details ..._pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein S100-A1
C: Protein S100-A1
H: Protein S100-A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,03310
Polymers31,6703
Non-polymers3637
Water25214
1
C: Protein S100-A1
hetero molecules

A: Protein S100-A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3967
Polymers21,1142
Non-polymers2825
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655y+1,x,-z1
Buried area2680 Å2
ΔGint-40 kcal/mol
Surface area10080 Å2
MethodPISA
2
H: Protein S100-A1
hetero molecules

H: Protein S100-A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2746
Polymers21,1142
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area3220 Å2
ΔGint-53 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.547, 53.547, 193.387
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 3 or (resid 4 and (name...
21(chain C and (resseq 3 or (resid 4 and (name...
31(chain H and (resseq 3 or (resid 4 and (name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERSERSER(chain A and (resseq 3 or (resid 4 and (name...AA33
12GLUGLUGLUGLU(chain A and (resseq 3 or (resid 4 and (name...AA44
13METMETPHEPHE(chain A and (resseq 3 or (resid 4 and (name...AA1 - 901 - 90
14METMETPHEPHE(chain A and (resseq 3 or (resid 4 and (name...AA1 - 901 - 90
15METMETPHEPHE(chain A and (resseq 3 or (resid 4 and (name...AA1 - 901 - 90
16METMETPHEPHE(chain A and (resseq 3 or (resid 4 and (name...AA1 - 901 - 90
17METMETPHEPHE(chain A and (resseq 3 or (resid 4 and (name...AA1 - 901 - 90
18METMETPHEPHE(chain A and (resseq 3 or (resid 4 and (name...AA1 - 901 - 90
21SERSERSERSER(chain C and (resseq 3 or (resid 4 and (name...CB33
22GLUGLUGLUGLU(chain C and (resseq 3 or (resid 4 and (name...CB44
23SERSERSERSER(chain C and (resseq 3 or (resid 4 and (name...CB3 - 943 - 94
24SERSERSERSER(chain C and (resseq 3 or (resid 4 and (name...CB3 - 943 - 94
25SERSERSERSER(chain C and (resseq 3 or (resid 4 and (name...CB3 - 943 - 94
26SERSERSERSER(chain C and (resseq 3 or (resid 4 and (name...CB3 - 943 - 94
27SERSERSERSER(chain C and (resseq 3 or (resid 4 and (name...CB3 - 943 - 94
28SERSERSERSER(chain C and (resseq 3 or (resid 4 and (name...CB3 - 943 - 94
31SERSERSERSER(chain H and (resseq 3 or (resid 4 and (name...HC33
32GLUGLUGLUGLU(chain H and (resseq 3 or (resid 4 and (name...HC44
33METMETSERSER(chain H and (resseq 3 or (resid 4 and (name...HC1 - 941 - 94
34METMETSERSER(chain H and (resseq 3 or (resid 4 and (name...HC1 - 941 - 94
35METMETSERSER(chain H and (resseq 3 or (resid 4 and (name...HC1 - 941 - 94
36METMETSERSER(chain H and (resseq 3 or (resid 4 and (name...HC1 - 941 - 94
37METMETSERSER(chain H and (resseq 3 or (resid 4 and (name...HC1 - 941 - 94
38METMETSERSER(chain H and (resseq 3 or (resid 4 and (name...HC1 - 941 - 94

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Components

#1: Protein Protein S100-A1 / / S-100 protein alpha chain / S-100 protein subunit alpha / S100 calcium-binding protein A1


Mass: 10556.783 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A1, S100A / Plasmid: pUC57 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23297
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 8000, calcium chloride, cacodylate / PH range: 7.00-7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.25→37.644 Å / Num. obs: 14767 / % possible obs: 92 % / Redundancy: 5.1 % / Biso Wilson estimate: 50.57 Å2 / Rsym value: 0.185 / Net I/σ(I): 14.45
Reflection shellResolution: 2.37→2.5 Å / Redundancy: 2 % / Rmerge(I) obs: 1.538 / Mean I/σ(I) obs: 0.5 / % possible all: 83

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Blu-Icedata collection
PDB_EXTRACT3.2data extraction
autoXDSdata reduction
SCALA3.3.20data scaling
Cootmodel building
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y5I

2y5i


Resolution: 2.249→37.644 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 45.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2905 757 5.13 %RANDOM
Rwork0.2746 14010 --
obs0.2754 14767 91.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 167.44 Å2 / Biso mean: 82.5976 Å2 / Biso min: 31.69 Å2
Refinement stepCycle: final / Resolution: 2.249→37.644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 14 14 2093
Biso mean--73.56 58.04 -
Num. residues----263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092097
X-RAY DIFFRACTIONf_angle_d0.9592815
X-RAY DIFFRACTIONf_chiral_restr0.059320
X-RAY DIFFRACTIONf_plane_restr0.006361
X-RAY DIFFRACTIONf_dihedral_angle_d24.733763
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A812X-RAY DIFFRACTION12.419TORSIONAL
12C812X-RAY DIFFRACTION12.419TORSIONAL
13H812X-RAY DIFFRACTION12.419TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2487-2.42230.4955770.45651888196563
2.4223-2.6660.45641490.41382893304297
2.666-3.05160.40771580.37752982314099
3.0516-3.84410.3232040.28993027323199
3.8441-37.64960.21651690.212132203389100
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)
17.73095.17041.19952.05530.07368.5629-0.19680.46110.4704-1.0934-0.37141.2618-0.2336-0.3073-0.02780.9832-0.1211-0.0030.498-0.03690.497839.955924.62460.5199
29.20692.84383.9597.29081.63676.3809-0.37130.94-0.0649-0.59470.2056-0.5065-0.28851.4560.09580.9687-0.05690.00410.7685-0.01480.371857.750733.26973.4781
32.01912.28190.95949.43111.1078.9235-0.1062-0.49871.04640.85270.1183-0.0505-0.69161.0850.30431.5244-0.5024-0.2743-0.3826-0.07970.513357.773337.303112.6531
49.3092-0.55052.18252.0154-1.22782.0043-0.3729-1.26480.99091.3399-0.4386-0.1621-0.33720.56820.55361.2447-0.1601-0.02990.7816-0.07760.467651.920436.112118.7182
58.19630.23043.9542.00337.48372.00630.4413-0.82430.09641.9848-0.1943-0.95950.45991.0483-0.2861.3409-0.0829-0.27631.09570.06350.645563.498729.268118.0276
62.03033.16184.25766.01382.14913.92450.34740.5563-0.92970.46370.2272-0.73180.80931.3439-0.60641.03750.0304-0.10020.6867-0.09260.458559.961924.36059.1742
75.79173.33695.31988.60932.32266.63680.8294-2.2679-0.02041.947-0.86121.02051.0209-0.5096-0.26891.6736-0.18820.04530.71260.13020.571843.280722.702320.2325
85.07675.9422-0.54932.0503-2.73866.0148-0.19520.1329-0.2613-0.83450.2129-0.79670.241-0.05370.31830.8104-0.03350.02750.98310.02020.442955.989648.5737-11.4324
94.19193.31483.39462.01151.48146.7299-0.34480.6064-0.1326-2.12590.3173-0.3211.5623-0.5974-0.1241.5443-0.1913-0.02041.1011-0.08030.397947.716634.0852-14.5509
103.98512.3351.92669.9527-1.74556.52790.21850.3218-0.03620.12590.18530.27331.1206-0.6705-0.13820.9909-0.2643-0.04540.8781-0.00410.385945.218135.8107-4.2429
111.64222.01781.22362.0237-2.20596.69580.2057-0.6482-0.04621.22730.39741.40940.7274-1.1763-0.44650.9141-0.27480.08791.3244-0.06521.036136.221639.6724-1.1081
126.47513.50842.08342.0065-1.21815.9049-0.26740.72350.3362-1.92160.83721.73750.7282-1.194-0.30831.2634-0.7687-0.39161.63650.04570.51938.417941.4005-15.0701
133.40392.62980.75252.0845-1.65686.15540.1964-0.15440.210.8320.10770.67390.0484-0.372-0.18970.9129-0.23730.04431.0710.07510.373444.522751.8927-3.3429
146.8793-1.1037-0.67651.9992-3.32342.00540.3395-0.58540.58833.1276-0.39341.135-2.0074-0.5250.00741.866-0.21110.091.57070.1920.556749.458462.91797.3802
156.00981.02671.05467.59131.09492.0066-0.2043-0.6753-0.54951.41980.4899-1.23050.8280.9394-0.44971.66260.09520.00580.9316-0.12180.219554.22845.891739.1864
163.83110.9492-1.49367.83412.01169.8446-0.3050.2210.16960.08260.4772-0.4941-1.5737-0.0446-0.27181.3673-0.11830.05840.7971-0.01660.449849.584557.250730.194
173.76941.044-0.54559.65733.98482.01-0.39990.58430.932-0.94280.29150.2693-3.3608-0.765-0.15112.00640.1701-0.05540.99650.07050.614143.281865.301924.627
184.9718-0.117-0.63127.0862.93572.0143-0.37040.85020.0425-0.9650.5631-0.5395-1.2884-0.1755-0.3291.5286-0.17060.00011.04160.0630.411748.233854.255318.302
194.8372-0.568-3.03865.25443.97682.0004-0.5461.0467-0.1172-1.37690.18470.8258-1.4741-2.30560.10441.64910.1059-0.27051.48250.11520.830535.681554.829816.8444
203.05870.1453-0.436.26542.67168.9662-0.26860.3721-0.0371-0.05210.20310.8745-0.415-1.81510.02631.1853-0.0084-0.0571.12090.06620.357840.242948.881626.3897
218.54496.71151.60576.45286.30391.9995-0.57060.4802-1.64680.63490.4526-0.81133.14590.1343-0.2352.0888-0.7503-0.6189-0.1549-1.2753-1.046749.43229.170223.6385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:10)A1 - 10
2X-RAY DIFFRACTION2(chain A and resid 11:31)A11 - 31
3X-RAY DIFFRACTION3(chain A and resid 32:39)A32 - 39
4X-RAY DIFFRACTION4(chain A and resid 40:47)A40 - 47
5X-RAY DIFFRACTION5(chain A and resid 53:63)A53 - 63
6X-RAY DIFFRACTION6(chain A and resid 64:81)A64 - 81
7X-RAY DIFFRACTION7(chain A and resid 82:90)A82 - 90
8X-RAY DIFFRACTION8(chain C and resid 3:16)C3 - 16
9X-RAY DIFFRACTION9(chain C and resid 17:28)C17 - 28
10X-RAY DIFFRACTION10(chain C and resid 29:42)C29 - 42
11X-RAY DIFFRACTION11(chain C and resid 43:63)C43 - 63
12X-RAY DIFFRACTION12(chain C and resid 64:73)C64 - 73
13X-RAY DIFFRACTION13(chain C and resid 74:89)C74 - 89
14X-RAY DIFFRACTION14(chain C and resid 90:94)C90 - 94
15X-RAY DIFFRACTION15(chain H and resid 1:9)H1 - 9
16X-RAY DIFFRACTION16(chain H and resid 10:21)H10 - 21
17X-RAY DIFFRACTION17(chain H and resid 22:32)H22 - 32
18X-RAY DIFFRACTION18(chain H and resid 33:45)H33 - 45
19X-RAY DIFFRACTION19(chain H and resid 46:65)H46 - 65
20X-RAY DIFFRACTION20(chain H and resid 66:89)H66 - 89
21X-RAY DIFFRACTION21(chain H and resid 90:94)H90 - 94

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