HEADER SUGAR BINDING PROTEIN 19-AUG-20 7JUH TITLE C-TYPE CARBOHYDRATE-RECOGNITION DOMAIN 4 OF THE MANNOSE RECEPTOR TITLE 2 COMPLEXED WITH MAN-ALPHA1-6MAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE MANNOSE RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MMR,C-TYPE LECTIN DOMAIN FAMILY 13 MEMBER D,C-TYPE LECTIN COMPND 5 DOMAIN FAMILY 13 MEMBER D-LIKE,HUMAN MANNOSE RECEPTOR,HMR,MACROPHAGE COMPND 6 MANNOSE RECEPTOR 1-LIKE PROTEIN 1; COMPND 7 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: MRC1, CLEC13D, CLEC13DL, MRC1L1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PT5T KEYWDS GLYCOBIOLOGY, CARBOHYDRATE-BINDING PROTEIN, C-TYPE LECTIN, COMPLEX, KEYWDS 2 SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.I.WEIS,H.FEINBERG REVDAT 5 23-OCT-24 7JUH 1 REMARK REVDAT 4 03-APR-24 7JUH 1 REMARK REVDAT 3 14-JUL-21 7JUH 1 JRNL REVDAT 2 17-FEB-21 7JUH 1 JRNL REVDAT 1 03-FEB-21 7JUH 0 JRNL AUTH H.FEINBERG,S.A.F.JEGOUZO,Y.LASANAJAK,D.F.SMITH,K.DRICKAMER, JRNL AUTH 2 W.I.WEIS,M.E.TAYLOR JRNL TITL STRUCTURAL ANALYSIS OF CARBOHYDRATE BINDING BY THE JRNL TITL 2 MACROPHAGE MANNOSE RECEPTOR CD206. JRNL REF J.BIOL.CHEM. V. 296 00368 2021 JRNL REFN ESSN 1083-351X JRNL PMID 33545173 JRNL DOI 10.1016/J.JBC.2021.100368 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 22710 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1127 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 31.7000 - 2.7995 0.98 2761 141 0.1556 0.1797 REMARK 3 2 2.7995 - 2.2222 0.98 2740 126 0.1694 0.2181 REMARK 3 3 2.2222 - 1.9414 0.98 2697 151 0.1431 0.1582 REMARK 3 4 1.9414 - 1.7639 0.97 2663 147 0.1382 0.1821 REMARK 3 5 1.7639 - 1.6374 0.98 2711 137 0.1350 0.1772 REMARK 3 6 1.6374 - 1.5409 0.98 2706 147 0.1294 0.1847 REMARK 3 7 1.5409 - 1.4637 0.96 2626 135 0.1432 0.1981 REMARK 3 8 1.4637 - 1.4000 0.98 2679 143 0.1747 0.2416 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7JUH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000249370. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22757 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 31.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.24200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PARTIALLY REFINED MODEL IN DIFFERENT SYMMETRY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 6.0MG/ML PROTEIN IN REMARK 280 5MM CACL2, 10MM TRIS, PH 8.0, 25MM NACL, AND 30MM MAN-ALPHA1-6- REMARK 280 MAN; RESERVOIR SOLUTION: 15% PEG 400, 0.1M MES PH=6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.52000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA A 627 REMARK 465 CYS A 628 REMARK 465 PRO A 629 REMARK 465 GLU A 630 REMARK 465 ASP A 631 REMARK 465 TRP A 632 REMARK 465 GLY A 633 REMARK 465 ALA A 634 REMARK 465 SER A 635 REMARK 465 SER A 636 REMARK 465 ARG A 637 REMARK 465 THR A 638 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 ASN A 720 50.61 -142.39 REMARK 500 ASN A 728 58.23 39.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1000 DISTANCE = 6.04 ANGSTROMS 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 802 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 671 O REMARK 620 2 SER A 671 OG 69.6 REMARK 620 3 ASN A 673 OD1 94.9 77.1 REMARK 620 4 GLU A 677 OE1 80.2 139.1 78.8 REMARK 620 5 GLU A 677 OE2 89.8 148.4 130.2 53.2 REMARK 620 6 HOH A 909 O 94.8 76.5 146.5 134.5 81.8 REMARK 620 7 HOH A 980 O 166.2 123.6 85.2 86.2 79.7 92.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 801 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 725 OE1 REMARK 620 2 ASN A 727 OD1 71.3 REMARK 620 3 GLU A 733 OE1 144.3 75.9 REMARK 620 4 ASN A 747 OD1 67.2 137.6 146.5 REMARK 620 5 ASP A 748 O 129.1 141.9 72.8 75.6 REMARK 620 6 ASP A 748 OD1 73.0 82.7 89.5 93.3 75.9 REMARK 620 7 MAN A 803 O3 74.0 76.5 111.6 83.9 135.7 145.2 REMARK 620 8 MAN A 803 O3 132.4 120.5 77.1 83.3 72.6 148.1 66.2 REMARK 620 9 MAN A 803 O4 131.4 120.2 77.9 82.9 73.5 149.1 65.2 1.1 REMARK 620 N 1 2 3 4 5 6 7 8 DBREF 7JUH A 628 761 UNP P22897 MRC1_HUMAN 646 779 SEQADV 7JUH ALA A 627 UNP P22897 EXPRESSION TAG SEQRES 1 A 135 ALA CYS PRO GLU ASP TRP GLY ALA SER SER ARG THR SER SEQRES 2 A 135 LEU CYS PHE LYS LEU TYR ALA LYS GLY LYS HIS GLU LYS SEQRES 3 A 135 LYS THR TRP PHE GLU SER ARG ASP PHE CYS ARG ALA LEU SEQRES 4 A 135 GLY GLY ASP LEU ALA SER ILE ASN ASN LYS GLU GLU GLN SEQRES 5 A 135 GLN THR ILE TRP ARG LEU ILE THR ALA SER GLY SER TYR SEQRES 6 A 135 HIS LYS LEU PHE TRP LEU GLY LEU THR TYR GLY SER PRO SEQRES 7 A 135 SER GLU GLY PHE THR TRP SER ASP GLY SER PRO VAL SER SEQRES 8 A 135 TYR GLU ASN TRP ALA TYR GLY GLU PRO ASN ASN TYR GLN SEQRES 9 A 135 ASN VAL GLU TYR CYS GLY GLU LEU LYS GLY ASP PRO THR SEQRES 10 A 135 MET SER TRP ASN ASP ILE ASN CYS GLU HIS LEU ASN ASN SEQRES 11 A 135 TRP ILE CYS GLN ILE HET CA A 801 1 HET CA A 802 1 HET MAN A 803 24 HETNAM CA CALCIUM ION HETNAM MAN ALPHA-D-MANNOPYRANOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 CA 2(CA 2+) FORMUL 4 MAN C6 H12 O6 FORMUL 5 HOH *100(H2 O) HELIX 1 AA1 GLY A 648 LYS A 652 5 5 HELIX 2 AA2 THR A 654 LEU A 665 1 12 HELIX 3 AA3 ASN A 674 GLY A 689 1 16 HELIX 4 AA4 ASN A 728 VAL A 732 5 5 SHEET 1 AA1 4 CYS A 641 TYR A 645 0 SHEET 2 AA1 4 ASN A 756 ILE A 761 -1 O ILE A 761 N CYS A 641 SHEET 3 AA1 4 LEU A 694 SER A 703 1 N TRP A 696 O ASN A 756 SHEET 4 AA1 4 GLY A 707 TRP A 710 -1 O GLY A 707 N SER A 703 SHEET 1 AA2 5 ASP A 668 LEU A 669 0 SHEET 2 AA2 5 ASN A 756 ILE A 761 -1 O GLN A 760 N ASP A 668 SHEET 3 AA2 5 LEU A 694 SER A 703 1 N TRP A 696 O ASN A 756 SHEET 4 AA2 5 CYS A 735 LYS A 739 -1 O LEU A 738 N PHE A 695 SHEET 5 AA2 5 TRP A 746 ILE A 749 -1 O ILE A 749 N CYS A 735 SSBOND 1 CYS A 662 CYS A 759 1555 1555 2.05 SSBOND 2 CYS A 735 CYS A 751 1555 1555 2.04 LINK O SER A 671 CA CA A 802 1555 1555 2.52 LINK OG SER A 671 CA CA A 802 1555 1555 2.54 LINK OD1 ASN A 673 CA CA A 802 1555 1555 2.25 LINK OE1 GLU A 677 CA CA A 802 1555 1555 2.44 LINK OE2 GLU A 677 CA CA A 802 1555 1555 2.46 LINK OE1 GLU A 725 CA CA A 801 1555 1555 2.53 LINK OD1 ASN A 727 CA CA A 801 1555 1555 2.37 LINK OE1 GLU A 733 CA CA A 801 1555 1555 2.47 LINK OD1 ASN A 747 CA CA A 801 1555 1555 2.42 LINK O ASP A 748 CA CA A 801 1555 1555 2.43 LINK OD1 ASP A 748 CA CA A 801 1555 1555 2.38 LINK CA CA A 801 O3 AMAN A 803 1555 1555 2.54 LINK CA CA A 801 O3 BMAN A 803 1555 1555 2.50 LINK CA CA A 801 O4 AMAN A 803 1555 1555 2.55 LINK CA CA A 801 O4 BMAN A 803 1555 1555 2.54 LINK CA CA A 802 O HOH A 909 1555 1555 2.27 LINK CA CA A 802 O HOH A 980 1555 1555 2.34 CISPEP 1 GLU A 725 PRO A 726 0 -2.93 CRYST1 31.922 59.040 34.846 90.00 114.48 90.00 P 1 21 1 2 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 0.031326 0.000000 0.014266 0.00000 SCALE2 0.000000 0.016938 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031534 0.00000