HEADER METAL BINDING PROTEIN 25-JUL-11 2LGF
TITLE SOLUTION STRUCTURE OF CA2+/CALMODULIN COMPLEXED WITH A PEPTIDE
TITLE 2 REPRESENTING THE CALMODULIN-BINDING DOMAIN OF L-SELECTIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CALMODULIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: SEQUENCE DATABASE RESIDUES 4-149;
COMPND 5 SYNONYM: CAM;
COMPND 6 ENGINEERED: YES;
COMPND 7 MOL_ID: 2;
COMPND 8 MOLECULE: L-SELECTIN;
COMPND 9 CHAIN: B;
COMPND 10 FRAGMENT: SEQUENCE DATABASE RESIDUES 349-363;
COMPND 11 SYNONYM: CD62 ANTIGEN-LIKE FAMILY MEMBER L, LEUKOCYTE ADHESION
COMPND 12 MOLECULE 1, LAM-1, LEUKOCYTE SURFACE ANTIGEN LEU-8, LEUKOCYTE-
COMPND 13 ENDOTHELIAL CELL ADHESION MOLECULE 1, LECAM1, LYMPH NODE HOMING
COMPND 14 RECEPTOR, TQ1, GP90-MEL;
COMPND 15 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2,
SOURCE 6 CAM3, CAMC, CAMIII;
SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET30B(+);
SOURCE 10 MOL_ID: 2;
SOURCE 11 SYNTHETIC: YES;
SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 13 ORGANISM_COMMON: HUMAN;
SOURCE 14 ORGANISM_TAXID: 9606
KEYWDS METAL BINDING PROTEIN
EXPDTA SOLUTION NMR
AUTHOR J.L.GIFFORD,H.ISHIDA,H.J.VOGEL
REVDAT 5 14-JUN-23 2LGF 1 REMARK LINK
REVDAT 4 27-APR-16 2LGF 1 ATOM REMARK SEQRES
REVDAT 3 29-AUG-12 2LGF 1 JRNL
REVDAT 2 22-AUG-12 2LGF 1 JRNL
REVDAT 1 13-JUN-12 2LGF 0
JRNL AUTH J.L.GIFFORD,H.ISHIDA,H.J.VOGEL
JRNL TITL STRUCTURAL INSIGHTS INTO CALMODULIN-REGULATED L-SELECTIN
JRNL TITL 2 ECTODOMAIN SHEDDING.
JRNL REF J.BIOL.CHEM. V. 287 26513 2012
JRNL REFN ISSN 0021-9258
JRNL PMID 22711531
JRNL DOI 10.1074/JBC.M112.373373
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRPIPE, CYANA, X-PLOR NIH
REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX
REMARK 3 (NMRPIPE), GUNTERT, MUMENTHALER AND WUTHRICH
REMARK 3 (CYANA), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE
REMARK 3 (X-PLOR NIH)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2LGF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-AUG-11.
REMARK 100 THE DEPOSITION ID IS D_1000102361.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303; 303
REMARK 210 PH : 6.8; 6.8
REMARK 210 IONIC STRENGTH : 0.1; 0.3
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.5-0.8 MM [U-13C; U-15N]
REMARK 210 PROTEIN_1, 0.5-0.8 MM PROTEIN_2,
REMARK 210 4 MM CALCIUM ION, 0.5 MM DSS,
REMARK 210 100 MM POTASSIUM CHLORIDE, 0.03 %
REMARK 210 SODIUM AZIDE, 20 MM BIS-TRIS,
REMARK 210 90% H2O/10% D2O; 0.5-0.8 MM [U-
REMARK 210 2H; U-15N] PROTEIN_1, 0.5-0.8 MM
REMARK 210 PROTEIN_2, 4 MM CALCIUM ION, 0.5
REMARK 210 MM DSS, 100 MM POTASSIUM
REMARK 210 CHLORIDE, 0.03 % SODIUM AZIDE,
REMARK 210 20 MM BIS-TRIS, 90% H2O/10% D2O;
REMARK 210 0.5-0.8 MM [1H/13C-METHYL MET; U-
REMARK 210 2H; U-15N] PROTEIN_1, 0.5-0.8 MM
REMARK 210 PROTEIN_2, 4 MM CALCIUM ION, 0.5
REMARK 210 MM DSS, 100 MM POTASSIUM
REMARK 210 CHLORIDE, 0.03 % SODIUM AZIDE,
REMARK 210 20 MM BIS-TRIS, 100% D2O; 0.5-
REMARK 210 0.8 MM [U-13C; U-15N] PROTEIN_1,
REMARK 210 0.5-0.8 MM PROTEIN_2, 4 MM
REMARK 210 CALCIUM ION, 0.5 MM DSS, 300 MM
REMARK 210 POTASSIUM CHLORIDE, 0.03 %
REMARK 210 SODIUM AZIDE, 20 MM BIS-TRIS, 90%
REMARK 210 H2O/10% D2O; 0.5-0.8 MM [U-13C;
REMARK 210 U-15N] PROTEIN_1, 0.5-0.8 MM
REMARK 210 PROTEIN_2, 4 MM CALCIUM ION, 0.5
REMARK 210 MM DSS, 300 MM POTASSIUM
REMARK 210 CHLORIDE, 0.03 % SODIUM AZIDE,
REMARK 210 20 MM BIS-TRIS, 16 W/V PF1 PHAGE,
REMARK 210 90% H2O/10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC;
REMARK 210 2D 1H-1H COSY; 3D CBCA(CO)NH; 3D
REMARK 210 C(CO)NH; 3D HNCO; 3D HNCACB; 3D
REMARK 210 HBHA(CO)NH; 3D H(CCO)NH; 3D 1H-
REMARK 210 13C NOESY; 3D HN(CA)CO; 2D HMBC;
REMARK 210 3D LRCH; F2-FILTERED 2D 1H-1H
REMARK 210 NOESY; 2D 1H-15N IPAP HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NMRVIEW, CYANA, X-PLOR NIH,
REMARK 210 PROCHECKNMR, TALOS, MOLMOL,
REMARK 210 XWINNMR
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS,
REMARK 210 SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 RES C SSSEQI
REMARK 465 ASP A 2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 HG SER A 81 H GLU A 84 1.32
REMARK 500 O ILE A 125 H ASP A 129 1.57
REMARK 500 O PHE A 12 H PHE A 16 1.58
REMARK 500 OD1 ASP A 20 H GLY A 23 1.60
REMARK 500 O GLU A 45 H GLN A 49 1.60
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 THR A 79 -14.95 -45.81
REMARK 500 ASN A 111 -2.40 -49.41
REMARK 500 PHE B 350 -22.35 -39.80
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 401 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 20 OD2
REMARK 620 2 ASP A 20 OD1 47.3
REMARK 620 3 ASP A 22 OD1 98.9 52.4
REMARK 620 4 ASP A 22 OD2 93.7 67.7 44.7
REMARK 620 5 ASP A 24 OD2 93.4 102.6 93.4 49.2
REMARK 620 6 ASP A 24 OD1 49.4 77.2 105.8 69.2 44.8
REMARK 620 7 THR A 26 O 53.5 100.3 152.4 127.8 89.1 58.5
REMARK 620 8 GLU A 31 OE2 112.1 81.1 61.8 104.9 146.0 158.1 123.9
REMARK 620 9 GLU A 31 OE1 108.2 112.7 110.0 150.1 144.5 140.6 82.1 48.4
REMARK 620 N 1 2 3 4 5 6 7 8
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 402 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 56 OD1
REMARK 620 2 ASP A 56 OD2 47.6
REMARK 620 3 ASP A 58 OD2 73.0 113.1
REMARK 620 4 ASP A 58 OD1 54.2 70.0 49.1
REMARK 620 5 ASN A 60 OD1 94.5 52.7 120.0 75.6
REMARK 620 6 THR A 62 O 107.6 65.1 174.2 126.4 54.4
REMARK 620 7 GLU A 67 OE2 114.2 139.1 86.6 135.3 146.2 98.2
REMARK 620 8 GLU A 67 OE1 77.0 90.4 105.4 128.4 129.1 80.2 49.0
REMARK 620 N 1 2 3 4 5 6 7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 403 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 93 OD2
REMARK 620 2 ASP A 93 OD1 42.9
REMARK 620 3 ASP A 95 OD1 86.9 48.2
REMARK 620 4 ASP A 95 OD2 130.8 97.1 49.0
REMARK 620 5 ASN A 97 OD1 53.5 55.2 59.0 81.8
REMARK 620 6 TYR A 99 O 69.8 107.4 123.0 112.8 65.6
REMARK 620 7 GLU A 104 OE1 109.0 129.1 146.9 120.0 153.1 90.0
REMARK 620 8 GLU A 104 OE2 123.9 105.0 97.9 87.8 155.7 138.5 49.1
REMARK 620 N 1 2 3 4 5 6 7
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 404 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 129 OD1
REMARK 620 2 ASP A 131 OD2 90.7
REMARK 620 3 ASP A 131 OD1 50.7 45.5
REMARK 620 4 ASP A 133 OD2 100.1 69.5 64.9
REMARK 620 5 ASP A 133 OD1 63.4 96.3 60.8 45.4
REMARK 620 6 GLN A 135 O 85.1 143.7 109.4 75.8 50.0
REMARK 620 7 GLU A 140 OE2 98.0 81.7 107.1 145.9 161.4 134.6
REMARK 620 8 GLU A 140 OE1 96.4 130.5 140.0 154.0 130.4 85.7 48.8
REMARK 620 N 1 2 3 4 5 6 7
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 404
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 17807 RELATED DB: BMRB
DBREF 2LGF A 2 148 UNP P62158 CALM_HUMAN 3 149
DBREF 2LGF B 349 363 UNP P14151 LYAM1_HUMAN 349 363
SEQRES 1 A 147 ASP GLN LEU THR GLU GLU GLN ILE ALA GLU PHE LYS GLU
SEQRES 2 A 147 ALA PHE SER LEU PHE ASP LYS ASP GLY ASP GLY THR ILE
SEQRES 3 A 147 THR THR LYS GLU LEU GLY THR VAL MET ARG SER LEU GLY
SEQRES 4 A 147 GLN ASN PRO THR GLU ALA GLU LEU GLN ASP MET ILE ASN
SEQRES 5 A 147 GLU VAL ASP ALA ASP GLY ASN GLY THR ILE ASP PHE PRO
SEQRES 6 A 147 GLU PHE LEU THR MET MET ALA ARG LYS MET LYS ASP THR
SEQRES 7 A 147 ASP SER GLU GLU GLU ILE ARG GLU ALA PHE ARG VAL PHE
SEQRES 8 A 147 ASP LYS ASP GLY ASN GLY TYR ILE SER ALA ALA GLU LEU
SEQRES 9 A 147 ARG HIS VAL MET THR ASN LEU GLY GLU LYS LEU THR ASP
SEQRES 10 A 147 GLU GLU VAL ASP GLU MET ILE ARG GLU ALA ASP ILE ASP
SEQRES 11 A 147 GLY ASP GLY GLN VAL ASN TYR GLU GLU PHE VAL GLN MET
SEQRES 12 A 147 MET THR ALA LYS
SEQRES 1 B 15 ALA PHE ILE ILE TRP LEU ALA ARG ARG LEU LYS LYS GLY
SEQRES 2 B 15 LYS LYS
HET CA A 401 1
HET CA A 402 1
HET CA A 403 1
HET CA A 404 1
HETNAM CA CALCIUM ION
FORMUL 3 CA 4(CA 2+)
HELIX 1 1 THR A 5 ASP A 20 1 16
HELIX 2 2 THR A 28 LEU A 39 1 12
HELIX 3 3 THR A 44 ASP A 56 1 13
HELIX 4 4 ASP A 64 ASP A 78 1 15
HELIX 5 5 SER A 81 ASP A 93 1 13
HELIX 6 6 SER A 101 ASN A 111 1 11
HELIX 7 7 THR A 117 ASP A 129 1 13
HELIX 8 8 ASN A 137 MET A 145 1 9
HELIX 9 9 ALA B 349 LYS B 363 1 15
LINK OD2 ASP A 20 CA CA A 401 1555 1555 2.65
LINK OD1 ASP A 20 CA CA A 401 1555 1555 2.71
LINK OD1 ASP A 22 CA CA A 401 1555 1555 2.61
LINK OD2 ASP A 22 CA CA A 401 1555 1555 2.98
LINK OD2 ASP A 24 CA CA A 401 1555 1555 2.65
LINK OD1 ASP A 24 CA CA A 401 1555 1555 2.95
LINK O THR A 26 CA CA A 401 1555 1555 2.60
LINK OE2 GLU A 31 CA CA A 401 1555 1555 2.61
LINK OE1 GLU A 31 CA CA A 401 1555 1555 2.65
LINK OD1 ASP A 56 CA CA A 402 1555 1555 2.60
LINK OD2 ASP A 56 CA CA A 402 1555 1555 2.73
LINK OD2 ASP A 58 CA CA A 402 1555 1555 2.59
LINK OD1 ASP A 58 CA CA A 402 1555 1555 2.60
LINK OD1 ASN A 60 CA CA A 402 1555 1555 2.59
LINK O THR A 62 CA CA A 402 1555 1555 2.56
LINK OE2 GLU A 67 CA CA A 402 1555 1555 2.59
LINK OE1 GLU A 67 CA CA A 402 1555 1555 2.61
LINK OD2 ASP A 93 CA CA A 403 1555 1555 2.63
LINK OD1 ASP A 93 CA CA A 403 1555 1555 3.12
LINK OD1 ASP A 95 CA CA A 403 1555 1555 2.59
LINK OD2 ASP A 95 CA CA A 403 1555 1555 2.61
LINK OD1 ASN A 97 CA CA A 403 1555 1555 2.60
LINK O TYR A 99 CA CA A 403 1555 1555 2.55
LINK OE1 GLU A 104 CA CA A 403 1555 1555 2.58
LINK OE2 GLU A 104 CA CA A 403 1555 1555 2.60
LINK OD1 ASP A 129 CA CA A 404 1555 1555 2.60
LINK OD2 ASP A 131 CA CA A 404 1555 1555 2.64
LINK OD1 ASP A 131 CA CA A 404 1555 1555 2.89
LINK OD2 ASP A 133 CA CA A 404 1555 1555 2.60
LINK OD1 ASP A 133 CA CA A 404 1555 1555 2.92
LINK O GLN A 135 CA CA A 404 1555 1555 2.62
LINK OE2 GLU A 140 CA CA A 404 1555 1555 2.59
LINK OE1 GLU A 140 CA CA A 404 1555 1555 2.62
SITE 1 AC1 5 ASP A 20 ASP A 22 ASP A 24 THR A 26
SITE 2 AC1 5 GLU A 31
SITE 1 AC2 5 ASP A 56 ASP A 58 ASN A 60 THR A 62
SITE 2 AC2 5 GLU A 67
SITE 1 AC3 5 ASP A 93 ASP A 95 ASN A 97 TYR A 99
SITE 2 AC3 5 GLU A 104
SITE 1 AC4 5 ASP A 129 ASP A 131 ASP A 133 GLN A 135
SITE 2 AC4 5 GLU A 140
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
(ATOM LINES ARE NOT SHOWN.)
END