HEADER PROTEIN TRANSPORT 13-JUN-19 6K8Q TITLE SOLUTION STRUCTURE OF THE INTERMEMBRANE SPACE DOMAIN OF THE TITLE 2 MITOCHONDRIAL IMPORT PROTEIN TIM21 FROM S. CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL IMPORT INNER MEMBRANE TRANSLOCASE SUBUNIT COMPND 3 TIM21; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: INTERMEMBRANE SPACE DOMAIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 GENE: TIM21, YGR033C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET28B(+) KEYWDS MEMBRANE, MITOCHONDRIA, TRANSLOCATION, PROTEIN TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.BALA,S.SHINYA,A.SRIVASTAVA,A.SHIMADA,N.KOBAYASHI,C.KOJIMA,F.TAMA, AUTHOR 2 O.MIYASHITA,D.KOHDA REVDAT 3 14-JUN-23 6K8Q 1 REMARK REVDAT 2 11-DEC-19 6K8Q 1 JRNL REVDAT 1 11-SEP-19 6K8Q 0 JRNL AUTH S.BALA,S.SHINYA,A.SRIVASTAVA,M.ISHIKAWA,A.SHIMADA, JRNL AUTH 2 N.KOBAYASHI,C.KOJIMA,F.TAMA,O.MIYASHITA,D.KOHDA JRNL TITL CRYSTAL CONTACT-FREE CONFORMATION OF AN INTRINSICALLY JRNL TITL 2 FLEXIBLE LOOP IN PROTEIN CRYSTAL: TIM21 AS THE CASE STUDY. JRNL REF BIOCHIM BIOPHYS ACTA GEN V.1864 29418 2020 JRNL REF 2 SUBJ JRNL REFN ISSN 1872-8006 JRNL PMID 31449839 JRNL DOI 10.1016/J.BBAGEN.2019.129418 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6K8Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1300012326. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 323 UM [U-13C; U-15N] TIM21, 20 REMARK 210 MM TRIS, 50 MM SODIUM CHLORIDE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HNCO; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HBHA(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, MAGRO-NMRVIEW, CYANA REMARK 210 METHOD USED : SIMULATED ANNEALING 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 O LYS A 59 H HIS A 67 1.55 REMARK 500 O MET A 101 H LEU A 113 1.57 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 26 -172.98 -58.56 REMARK 500 1 ASP A 28 94.45 175.68 REMARK 500 1 GLU A 41 -137.83 -110.37 REMARK 500 1 THR A 44 32.93 -164.69 REMARK 500 1 ASN A 45 -156.83 -149.52 REMARK 500 1 LYS A 47 -163.38 55.13 REMARK 500 1 ARG A 50 94.09 -171.72 REMARK 500 1 LYS A 79 -171.09 -175.88 REMARK 500 1 LYS A 91 -79.64 63.92 REMARK 500 1 GLN A 92 124.73 168.95 REMARK 500 1 TYR A 94 -164.48 -124.86 REMARK 500 1 ILE A 114 -80.40 -121.57 REMARK 500 2 ASP A 28 78.47 -179.26 REMARK 500 2 GLU A 41 -136.88 -85.35 REMARK 500 2 LEU A 42 108.52 -38.71 REMARK 500 2 ASN A 45 101.11 56.95 REMARK 500 2 ASP A 46 -158.13 168.92 REMARK 500 2 LYS A 47 -163.32 -55.82 REMARK 500 2 THR A 49 -94.55 42.54 REMARK 500 2 ARG A 50 99.46 58.25 REMARK 500 2 LYS A 79 -179.81 177.05 REMARK 500 2 LYS A 91 -140.20 63.09 REMARK 500 2 GLN A 92 -165.85 -54.13 REMARK 500 2 ASN A 93 30.90 -89.97 REMARK 500 2 TYR A 94 -160.16 -60.26 REMARK 500 3 SER A 2 -70.27 64.32 REMARK 500 3 ASP A 28 89.35 -178.07 REMARK 500 3 GLU A 41 -158.75 -84.73 REMARK 500 3 LEU A 42 125.03 59.10 REMARK 500 3 THR A 44 -39.72 -164.11 REMARK 500 3 ASP A 46 23.76 -142.41 REMARK 500 3 LYS A 47 179.37 57.99 REMARK 500 3 ARG A 50 -161.41 -57.61 REMARK 500 3 LYS A 79 -161.12 -178.58 REMARK 500 3 LYS A 91 -83.63 51.64 REMARK 500 3 GLN A 92 68.93 -164.02 REMARK 500 3 ASN A 93 78.48 -113.44 REMARK 500 3 TYR A 94 -138.54 46.78 REMARK 500 4 ASP A 28 84.66 174.10 REMARK 500 4 GLU A 41 -150.66 -130.42 REMARK 500 4 LEU A 42 -167.55 -161.05 REMARK 500 4 ILE A 43 -173.54 -51.87 REMARK 500 4 ASP A 46 -165.68 -108.65 REMARK 500 4 LYS A 47 -155.55 -83.45 REMARK 500 4 ARG A 50 38.69 -165.58 REMARK 500 4 ASN A 51 51.16 -141.73 REMARK 500 4 LYS A 79 -167.74 179.74 REMARK 500 4 LYS A 91 -161.28 44.42 REMARK 500 4 TYR A 94 -176.05 -171.71 REMARK 500 4 ILE A 114 -52.04 -133.64 REMARK 500 REMARK 500 THIS ENTRY HAS 245 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36264 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE INTERMEMBRANE SPACE DOMAIN OF THE REMARK 900 MITOCHONDRIAL IMPORT PROTEIN TIM21 FROM S. CEREVISIAE DBREF 6K8Q A 3 115 UNP P53220 TIM21_YEAST 105 217 SEQADV 6K8Q GLY A 1 UNP P53220 EXPRESSION TAG SEQADV 6K8Q SER A 2 UNP P53220 EXPRESSION TAG SEQRES 1 A 115 GLY SER ASP THR GLN LEU PHE ASN ARG ALA VAL SER MET SEQRES 2 A 115 VAL GLU LYS ASN LYS ASP ILE ARG SER LEU LEU GLN CYS SEQRES 3 A 115 ASP ASP GLY ILE THR GLY LYS GLU ARG LEU LYS ALA TYR SEQRES 4 A 115 GLY GLU LEU ILE THR ASN ASP LYS TRP THR ARG ASN ARG SEQRES 5 A 115 PRO ILE VAL SER THR LYS LYS LEU ASP LYS GLU GLY ARG SEQRES 6 A 115 THR HIS HIS TYR MET ARG PHE HIS VAL GLU SER LYS LYS SEQRES 7 A 115 LYS ILE ALA LEU VAL HIS LEU GLU ALA LYS GLU SER LYS SEQRES 8 A 115 GLN ASN TYR GLN PRO ASP PHE ILE ASN MET TYR VAL ASP SEQRES 9 A 115 VAL PRO GLY GLU LYS ARG TYR TYR LEU ILE LYS HELIX 1 AA1 GLY A 1 ASN A 17 1 17 HELIX 2 AA2 ASN A 17 LEU A 24 1 8 SHEET 1 AA1 3 LYS A 37 TYR A 39 0 SHEET 2 AA1 3 THR A 66 GLU A 75 -1 O GLU A 75 N LYS A 37 SHEET 3 AA1 3 THR A 57 LEU A 60 -1 N LYS A 59 O HIS A 67 SHEET 1 AA2 5 LYS A 37 TYR A 39 0 SHEET 2 AA2 5 THR A 66 GLU A 75 -1 O GLU A 75 N LYS A 37 SHEET 3 AA2 5 ILE A 80 GLU A 89 -1 O ALA A 81 N VAL A 74 SHEET 4 AA2 5 PRO A 96 ASP A 104 -1 O ASP A 97 N LYS A 88 SHEET 5 AA2 5 TYR A 111 TYR A 112 -1 O TYR A 111 N VAL A 103 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