HEADER METAL BINDING PROTEIN 28-JAN-19 6QK5 TITLE SOLUTION STRUCTURE OF THE ZN-LOADED FORM OF A METALLOTHIONEIN FROM TITLE 2 HELIX POMATIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CADMIUM-METALLOTHIONEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CD-MT; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE FIRST RESIDUE GLY IS AN ARTEFACT FROM CLONING SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELIX POMATIA; SOURCE 3 ORGANISM_COMMON: ROMAN SNAIL; SOURCE 4 ORGANISM_TAXID: 6536; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PLYS KEYWDS METALLOTHIONEIN, CADMIUM PROTEIN, SNAIL PROTEIN, HELIX POMATIA, METAL KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR O.ZERBE,S.JURT,A.BEIL REVDAT 4 14-JUN-23 6QK5 1 REMARK REVDAT 3 01-JUL-20 6QK5 1 JRNL REVDAT 2 15-JAN-20 6QK5 1 JRNL REVDAT 1 18-DEC-19 6QK5 0 JRNL AUTH A.BEIL,S.JURT,R.WALSER,T.SCHONHUT,P.GUNTERT,O.PALACIOS, JRNL AUTH 2 S.ATRIAN,M.CAPDEVILA,R.DALLINGER,O.ZERBE JRNL TITL THE SOLUTION STRUCTURE AND DYNAMICS OF CD-METALLOTHIONEIN JRNL TITL 2 FROMHELIX POMATIAREVEAL OPTIMIZATION FOR BINDING CD OVER ZN. JRNL REF BIOCHEMISTRY V. 58 4570 2019 JRNL REFN ISSN 0006-2960 JRNL PMID 31633358 JRNL DOI 10.1021/ACS.BIOCHEM.9B00830 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS, X-PLOR REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. (CNS), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6QK5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1292100177. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 10 MM [U-2H] TRIS, 1 MM TSP, 90% REMARK 210 H2O/10% D2O; 10 MM [U-2H] TRIS, REMARK 210 1 MM TSP, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HCCH-TOCSY; 3D 1H-15N REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, CCPNMR ANALYSIS, CARA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: MONOMERIC 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 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 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 1 CYS A 25 79.42 53.83 REMARK 500 1 ALA A 35 -50.80 -125.70 REMARK 500 2 GLU A 8 -67.00 -143.40 REMARK 500 2 CYS A 25 92.61 59.96 REMARK 500 2 ALA A 35 -64.43 -121.72 REMARK 500 2 LYS A 37 58.38 -93.32 REMARK 500 2 SER A 57 26.44 -148.07 REMARK 500 3 CYS A 25 94.60 57.30 REMARK 500 4 GLU A 8 -82.39 -138.62 REMARK 500 4 CYS A 25 104.39 66.72 REMARK 500 4 ALA A 35 -69.09 -104.62 REMARK 500 4 SER A 62 164.72 66.14 REMARK 500 4 SER A 63 -14.32 69.31 REMARK 500 5 CYS A 25 101.18 63.48 REMARK 500 5 ALA A 35 -72.06 -106.45 REMARK 500 5 THR A 38 -173.04 -171.70 REMARK 500 5 SER A 62 166.39 65.65 REMARK 500 5 SER A 63 -16.57 70.21 REMARK 500 6 CYS A 25 81.90 53.59 REMARK 500 6 ALA A 35 -53.55 -120.71 REMARK 500 6 SER A 62 171.99 62.99 REMARK 500 7 GLU A 8 -85.70 -73.03 REMARK 500 7 CYS A 25 90.94 55.90 REMARK 500 7 CYS A 31 -76.70 -124.90 REMARK 500 7 ALA A 35 -63.81 -131.55 REMARK 500 7 LYS A 37 50.94 -118.79 REMARK 500 7 THR A 53 76.27 50.45 REMARK 500 8 LYS A 4 -65.60 -97.17 REMARK 500 8 LYS A 9 52.12 -90.89 REMARK 500 8 CYS A 25 103.78 65.59 REMARK 500 9 GLU A 8 -93.71 -100.43 REMARK 500 9 CYS A 25 99.36 64.84 REMARK 500 9 GLU A 29 0.00 -160.77 REMARK 500 9 ALA A 35 -67.23 -102.49 REMARK 500 9 LYS A 37 45.19 -105.71 REMARK 500 10 CYS A 25 105.83 66.54 REMARK 500 10 CYS A 27 -164.81 -124.25 REMARK 500 10 ALA A 35 -58.17 -126.17 REMARK 500 10 THR A 53 72.79 50.78 REMARK 500 11 LYS A 4 -66.78 -93.05 REMARK 500 11 LYS A 9 -40.48 176.82 REMARK 500 11 LYS A 24 -46.18 -130.49 REMARK 500 11 CYS A 25 82.29 64.06 REMARK 500 11 GLU A 29 -175.19 66.14 REMARK 500 12 LYS A 24 -43.28 -146.19 REMARK 500 12 CYS A 25 74.12 67.24 REMARK 500 12 SER A 62 170.28 63.77 REMARK 500 12 SER A 63 -25.16 70.87 REMARK 500 13 CYS A 25 99.22 65.53 REMARK 500 13 SER A 57 26.36 -142.58 REMARK 500 REMARK 500 THIS ENTRY HAS 93 RAMACHANDRAN OUTLIERS. 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 ZN A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 10 SG REMARK 620 2 CYS A 14 SG 108.8 REMARK 620 3 CYS A 27 SG 111.8 99.1 REMARK 620 4 CYS A 31 SG 113.6 113.0 109.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 14 SG REMARK 620 2 CYS A 19 SG 111.2 REMARK 620 3 CYS A 33 SG 113.6 103.3 REMARK 620 4 CYS A 36 SG 109.5 104.8 113.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 103 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 21 SG REMARK 620 2 CYS A 25 SG 110.6 REMARK 620 3 CYS A 27 SG 108.5 111.4 REMARK 620 4 CYS A 36 SG 105.2 103.9 116.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 104 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 39 SG REMARK 620 2 CYS A 52 SG 107.7 REMARK 620 3 CYS A 58 SG 108.6 107.8 REMARK 620 4 CYS A 66 SG 106.6 115.9 110.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 106 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 41 SG REMARK 620 2 CYS A 46 SG 108.8 REMARK 620 3 CYS A 48 SG 115.6 110.8 REMARK 620 4 CYS A 52 SG 106.7 109.2 105.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 105 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 48 SG REMARK 620 2 CYS A 60 SG 115.6 REMARK 620 3 CYS A 64 SG 110.0 106.0 REMARK 620 4 CYS A 66 SG 105.6 104.3 115.6 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 106 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34355 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE ZN-LOADED FORM OF A METALLOTHIONEIN FROM REMARK 900 HELIX POMATIA DBREF 6QK5 A 2 67 UNP P33187 MTCD_HELPO 1 66 SEQADV 6QK5 GLY A 1 UNP P33187 EXPRESSION TAG SEQRES 1 A 67 GLY SER GLY LYS GLY LYS GLY GLU LYS CYS THR SER ALA SEQRES 2 A 67 CYS ARG SER GLU PRO CYS GLN CYS GLY SER LYS CYS GLN SEQRES 3 A 67 CYS GLY GLU GLY CYS THR CYS ALA ALA CYS LYS THR CYS SEQRES 4 A 67 ASN CYS THR SER ASP GLY CYS LYS CYS GLY LYS GLU CYS SEQRES 5 A 67 THR GLY PRO ASP SER CYS LYS CYS GLY SER SER CYS SER SEQRES 6 A 67 CYS LYS HET ZN A 101 1 HET ZN A 102 1 HET ZN A 103 1 HET ZN A 104 1 HET ZN A 105 1 HET ZN A 106 1 HETNAM ZN ZINC ION FORMUL 2 ZN 6(ZN 2+) HELIX 1 AA1 GLY A 54 CYS A 58 5 5 LINK SG CYS A 10 ZN ZN A 101 1555 1555 2.37 LINK SG CYS A 14 ZN ZN A 101 1555 1555 2.56 LINK SG CYS A 14 ZN ZN A 102 1555 1555 2.27 LINK SG CYS A 19 ZN ZN A 102 1555 1555 2.48 LINK SG CYS A 21 ZN ZN A 103 1555 1555 2.45 LINK SG CYS A 25 ZN ZN A 103 1555 1555 2.48 LINK SG CYS A 27 ZN ZN A 101 1555 1555 2.52 LINK SG CYS A 27 ZN ZN A 103 1555 1555 2.25 LINK SG CYS A 31 ZN ZN A 101 1555 1555 2.36 LINK SG CYS A 33 ZN ZN A 102 1555 1555 2.39 LINK SG CYS A 36 ZN ZN A 102 1555 1555 2.51 LINK SG CYS A 36 ZN ZN A 103 1555 1555 2.54 LINK SG CYS A 39 ZN ZN A 104 1555 1555 2.32 LINK SG CYS A 41 ZN ZN A 106 1555 1555 2.32 LINK SG CYS A 46 ZN ZN A 106 1555 1555 2.33 LINK SG CYS A 48 ZN ZN A 105 1555 1555 2.51 LINK SG CYS A 48 ZN ZN A 106 1555 1555 2.28 LINK SG CYS A 52 ZN ZN A 104 1555 1555 2.59 LINK SG CYS A 52 ZN ZN A 106 1555 1555 2.34 LINK SG CYS A 58 ZN ZN A 104 1555 1555 2.54 LINK SG CYS A 60 ZN ZN A 105 1555 1555 2.46 LINK SG CYS A 64 ZN ZN A 105 1555 1555 2.35 LINK SG CYS A 66 ZN ZN A 104 1555 1555 2.50 LINK SG CYS A 66 ZN ZN A 105 1555 1555 2.30 CISPEP 1 GLU A 17 PRO A 18 1 0.35 CISPEP 2 GLU A 17 PRO A 18 2 0.47 CISPEP 3 GLU A 17 PRO A 18 3 -2.12 CISPEP 4 GLU A 17 PRO A 18 4 -0.52 CISPEP 5 GLU A 17 PRO A 18 5 -0.33 CISPEP 6 GLU A 17 PRO A 18 6 -2.26 CISPEP 7 GLU A 17 PRO A 18 7 -0.16 CISPEP 8 GLU A 17 PRO A 18 8 -1.18 CISPEP 9 GLU A 17 PRO A 18 9 -2.25 CISPEP 10 GLU A 17 PRO A 18 10 -1.77 CISPEP 11 GLU A 17 PRO A 18 11 0.89 CISPEP 12 GLU A 17 PRO A 18 12 -0.95 CISPEP 13 GLU A 17 PRO A 18 13 0.06 CISPEP 14 GLU A 17 PRO A 18 14 -0.80 CISPEP 15 GLU A 17 PRO A 18 15 1.52 CISPEP 16 GLU A 17 PRO A 18 16 0.11 CISPEP 17 GLU A 17 PRO A 18 17 0.33 CISPEP 18 GLU A 17 PRO A 18 18 0.70 CISPEP 19 GLU A 17 PRO A 18 19 1.80 CISPEP 20 GLU A 17 PRO A 18 20 -0.46 SITE 1 AC1 4 CYS A 10 CYS A 14 CYS A 27 CYS A 31 SITE 1 AC2 4 CYS A 14 CYS A 19 CYS A 33 CYS A 36 SITE 1 AC3 5 CYS A 21 CYS A 25 CYS A 27 CYS A 36 SITE 2 AC3 5 LYS A 37 SITE 1 AC4 6 CYS A 39 CYS A 52 CYS A 58 CYS A 66 SITE 2 AC4 6 ZN A 105 ZN A 106 SITE 1 AC5 6 CYS A 48 LYS A 50 CYS A 60 CYS A 64 SITE 2 AC5 6 CYS A 66 ZN A 104 SITE 1 AC6 5 CYS A 41 CYS A 46 CYS A 48 CYS A 52 SITE 2 AC6 5 ZN A 104 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 MODEL 1