HEADER METAL BINDING PROTEIN 12-JAN-15 2MXP TITLE SOLUTION STRUCTURE OF NDP52 UBIQUITIN-BINDING ZINC FINGER COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN COMPND 3 2; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: C-TERMINAL, UNP RESIDUES 414-446; COMPND 6 SYNONYM: ANTIGEN NUCLEAR DOT 52 KDA PROTEIN, NUCLEAR DOMAIN 10 COMPND 7 PROTEIN NDP52, NUCLEAR DOMAIN 10 PROTEIN 52, NUCLEAR DOT PROTEIN 52; COMPND 8 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: CALCOCO2, NDP52; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET32A KEYWDS ZINC FINGER, NDP52, UBIQUITIN-BINDING, C2H2-TYPE, METAL BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.PAN,X.XIE REVDAT 3 15-MAY-24 2MXP 1 REMARK REVDAT 2 14-JUN-23 2MXP 1 REMARK LINK REVDAT 1 11-NOV-15 2MXP 0 JRNL AUTH X.XIE,F.LI,Y.WANG,Y.WANG,Z.LIN,X.CHENG,J.LIU,C.CHEN,L.PAN JRNL TITL MOLECULAR BASIS OF UBIQUITIN RECOGNITION BY THE AUTOPHAGY JRNL TITL 2 RECEPTOR CALCOCO2 JRNL REF AUTOPHAGY V. 11 1775 2015 JRNL REFN ISSN 1554-8627 JRNL PMID 26506893 JRNL DOI 10.1080/15548627.2015.1082025 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, CNS REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MXP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000104174. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 0.1; 0.1 REMARK 210 PRESSURE : AMBIENT ATM; AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 ENTITY_1-1, 1 MM [U-100% 15N] REMARK 210 ENTITY_1-2, 90% H2O/10% D2O; 1 REMARK 210 MM [U-100% 13C; U-100% 15N] REMARK 210 ENTITY_1-3, 100% D2O; 1.2 MM REMARK 210 ENTITY_1-4, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D CBCA(CO)NH; 3D HNCACB; 3D 1H REMARK 210 -15N NOESY; 2D 1H-13C HSQC; 3D REMARK 210 HCCH-TOCSY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PIPP, SPARKY, CNS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: 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 GLN A 51 112.32 61.09 REMARK 500 1 PRO A 52 74.26 -62.06 REMARK 500 1 CYS A 54 140.94 -177.67 REMARK 500 1 ASP A 61 19.38 86.59 REMARK 500 2 MET A 50 150.21 62.24 REMARK 500 2 PRO A 52 174.64 -54.30 REMARK 500 2 CYS A 54 147.36 177.68 REMARK 500 2 ASP A 61 24.76 82.14 REMARK 500 2 GLU A 68 33.07 -97.88 REMARK 500 3 MET A 50 -46.57 -165.50 REMARK 500 3 CYS A 54 -174.26 178.17 REMARK 500 3 ASP A 61 36.92 80.10 REMARK 500 4 CYS A 54 141.28 176.81 REMARK 500 4 ASP A 61 38.67 78.18 REMARK 500 5 ASP A 61 -37.94 153.86 REMARK 500 5 LYS A 62 127.54 -31.20 REMARK 500 5 GLU A 68 35.13 -98.92 REMARK 500 6 CYS A 54 -179.14 179.47 REMARK 500 6 ASP A 61 -37.93 153.11 REMARK 500 6 LYS A 62 126.32 -30.72 REMARK 500 6 GLU A 68 33.21 -97.45 REMARK 500 7 PRO A 52 76.21 -69.59 REMARK 500 7 CYS A 54 -173.28 -170.32 REMARK 500 7 ASP A 61 17.53 82.45 REMARK 500 7 LYS A 62 171.38 -59.27 REMARK 500 8 CYS A 54 140.86 -172.85 REMARK 500 8 ASP A 61 38.09 78.94 REMARK 500 9 MET A 50 74.47 -103.34 REMARK 500 9 LEU A 53 32.36 74.40 REMARK 500 9 ASP A 61 13.68 86.79 REMARK 500 10 GLN A 51 85.24 -153.81 REMARK 500 10 PRO A 52 -170.20 -54.31 REMARK 500 10 CYS A 54 -175.50 175.76 REMARK 500 10 ASP A 61 39.67 76.67 REMARK 500 11 MET A 50 -39.42 -177.11 REMARK 500 11 GLN A 51 69.89 60.64 REMARK 500 11 PRO A 52 171.96 -56.41 REMARK 500 11 ASP A 61 7.89 96.52 REMARK 500 12 MET A 50 -52.02 -176.97 REMARK 500 12 GLN A 51 147.02 61.82 REMARK 500 12 CYS A 54 -175.63 171.62 REMARK 500 12 ASP A 61 12.60 85.46 REMARK 500 12 GLU A 68 35.52 -99.41 REMARK 500 13 MET A 50 97.87 59.98 REMARK 500 13 PRO A 52 76.99 -67.81 REMARK 500 13 CYS A 54 139.06 -176.44 REMARK 500 13 ASP A 61 33.90 84.51 REMARK 500 13 GLU A 68 32.43 -97.63 REMARK 500 14 MET A 50 -66.44 -160.35 REMARK 500 14 GLN A 51 102.56 -48.90 REMARK 500 REMARK 500 THIS ENTRY HAS 75 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 57 SG REMARK 620 2 CYS A 60 SG 121.1 REMARK 620 3 HIS A 75 NE2 102.2 107.7 REMARK 620 4 HIS A 79 NE2 108.3 116.6 97.0 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XKL RELATED DB: PDB REMARK 900 RELATED ID: 25423 RELATED DB: BMRB DBREF 2MXP A 49 81 UNP Q13137 CACO2_HUMAN 414 446 SEQRES 1 A 33 GLN MET GLN PRO LEU CYS PHE ASN CYS PRO ILE CYS ASP SEQRES 2 A 33 LYS ILE PHE PRO ALA THR GLU LYS GLN ILE PHE GLU ASP SEQRES 3 A 33 HIS VAL PHE CYS HIS SER LEU HET ZN A 101 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 GLU A 68 SER A 80 1 13 SHEET 1 A 2 CYS A 54 ASN A 56 0 SHEET 2 A 2 ILE A 63 PRO A 65 -1 O PHE A 64 N PHE A 55 LINK SG CYS A 57 ZN ZN A 101 1555 1555 2.30 LINK SG CYS A 60 ZN ZN A 101 1555 1555 2.29 LINK NE2 HIS A 75 ZN ZN A 101 1555 1555 1.97 LINK NE2 HIS A 79 ZN ZN A 101 1555 1555 2.02 SITE 1 AC1 4 CYS A 57 CYS A 60 HIS A 75 HIS A 79 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