HEADER ENDOCYTOSIS 31-OCT-17 5YOZ TITLE SOLUTION STRUCTURE OF TRUNCATED RAB5A FROM LEISHMANIA DONOVANI COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAB5A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LEISHMANIA DONOVANI; SOURCE 3 ORGANISM_TAXID: 5661; SOURCE 4 GENE: RAB5A; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS RAB, GTPASE, EARLY ENDOCYTOSIS, GTP HYDROLYSING ACTIVITY, ENDOCYTOSIS EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR D.MAHESHWARI,R.YADAV,A.MUKHOPADHYAY,A.ARORA REVDAT 2 14-JUN-23 5YOZ 1 REMARK REVDAT 1 24-OCT-18 5YOZ 0 JRNL AUTH D.MAHESHWARI,R.YADAV,R.RASTOGI,A.JAIN,S.TRIPATHI, JRNL AUTH 2 A.MUKHOPADHYAY,A.ARORA JRNL TITL STRUCTURAL AND BIOPHYSICAL CHARACTERIZATION OF RAB5A FROM JRNL TITL 2 LEISHMANIA DONOVANI JRNL REF BIOPHYS. J. V. 115 1217 2018 JRNL REFN ESSN 1542-0086 JRNL PMID 30241678 JRNL DOI 10.1016/J.BPJ.2018.08.032 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5YOZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-NOV-17. REMARK 100 THE DEPOSITION ID IS D_1300005653. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 20 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 5 MM MAGNESIUM REMARK 210 CHLORIDE, 1 MM GTP, 2 MM DTT, 3 % REMARK 210 GLYCEROL, 0.1 % SODIUM AZIDE, REMARK 210 95% H2O/5% D2O; 20 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 5 MM MAGNESIUM CHLORIDE, 1 MM REMARK 210 GTP, 2 MM DTT, 3 % GLYCEROL, 0.1 REMARK 210 % SODIUM AZIDE, 95% H2O/5% 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; 2D CBHE; 2D CBHD; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HNCO; REMARK 210 3D HN(CA)CO; 3D H(CCO)NH; 3D REMARK 210 C(CO)NH; 3D 1H-15N NOESY; 3D 1H- REMARK 210 15N TOCSY; 3D HCCH-TOCSY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-13C REMARK 210 NOESY AROMATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, CARA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 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 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 SER A 0 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 HB3 LEU A 39 HB2 GLN A 42 1.25 REMARK 500 OE2 GLU A 99 HZ3 LYS A 102 1.59 REMARK 500 OD2 ASP A 116 HG SER A 118 1.60 REMARK 500 HZ3 LYS A 128 OD1 ASP A 160 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 1 ALA A 11 80.10 72.49 REMARK 500 1 LEU A 19 -162.34 -116.25 REMARK 500 1 LEU A 72 85.39 -153.86 REMARK 500 1 ARG A 84 37.31 -72.61 REMARK 500 1 ALA A 115 -108.41 -104.95 REMARK 500 1 LYS A 127 87.17 64.35 REMARK 500 1 ASN A 161 -14.98 71.98 REMARK 500 1 ASN A 162 -5.98 73.97 REMARK 500 1 LYS A 174 -65.89 -94.71 REMARK 500 2 ASN A 2 85.00 56.29 REMARK 500 2 ALA A 11 43.53 169.41 REMARK 500 2 ALA A 24 30.33 -88.28 REMARK 500 2 THR A 34 -70.21 -71.49 REMARK 500 2 ASN A 36 66.58 60.55 REMARK 500 2 ASN A 41 57.00 -111.47 REMARK 500 2 ILE A 46 138.44 -172.85 REMARK 500 2 ALA A 48 105.55 -175.71 REMARK 500 2 ALA A 115 -118.34 -89.20 REMARK 500 2 LYS A 127 92.55 57.32 REMARK 500 2 ASN A 161 -6.56 72.41 REMARK 500 2 ASN A 162 -46.83 73.72 REMARK 500 3 ALA A 70 43.88 -78.99 REMARK 500 3 ALA A 115 -130.48 -93.26 REMARK 500 3 LYS A 127 91.02 74.74 REMARK 500 3 LEU A 133 33.39 -94.98 REMARK 500 3 ASN A 161 -13.78 77.46 REMARK 500 3 ASN A 162 -10.97 70.82 REMARK 500 3 LYS A 174 -77.61 -102.95 REMARK 500 4 ASN A 2 86.28 60.34 REMARK 500 4 LEU A 19 -155.96 -126.15 REMARK 500 4 LEU A 72 62.38 -104.25 REMARK 500 4 ALA A 115 -106.95 -110.99 REMARK 500 4 LYS A 127 97.30 69.14 REMARK 500 4 GLN A 149 36.62 74.68 REMARK 500 4 ASN A 162 -17.80 67.89 REMARK 500 5 PRO A 6 108.82 -58.45 REMARK 500 5 ALA A 11 100.18 -176.01 REMARK 500 5 ASN A 41 46.04 -84.71 REMARK 500 5 ALA A 48 156.86 64.20 REMARK 500 5 LEU A 72 -90.01 -90.46 REMARK 500 5 ALA A 115 -145.20 -97.84 REMARK 500 5 GLN A 149 62.90 67.91 REMARK 500 5 ASN A 161 -0.82 79.83 REMARK 500 5 ASN A 162 -49.12 75.80 REMARK 500 5 LYS A 174 -68.99 -126.25 REMARK 500 6 ALA A 11 84.76 63.62 REMARK 500 6 ASN A 41 57.12 -97.88 REMARK 500 6 ALA A 115 -136.39 -80.92 REMARK 500 6 LYS A 127 64.55 70.55 REMARK 500 6 ASN A 161 -2.20 68.56 REMARK 500 REMARK 500 THIS ENTRY HAS 88 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27192 RELATED DB: BMRB DBREF1 5YOZ A 1 175 UNP A0A109NYM0_LEIDO DBREF2 5YOZ A A0A109NYM0 1 195 SEQADV 5YOZ GLY A -1 UNP A0A109NYM EXPRESSION TAG SEQADV 5YOZ SER A 0 UNP A0A109NYM EXPRESSION TAG SEQADV 5YOZ ASP A 58 UNP A0A109NYM PRO 58 ENGINEERED MUTATION SEQADV 5YOZ GLY A 59 UNP A0A109NYM PRO 59 ENGINEERED MUTATION SEQADV 5YOZ A UNP A0A109NYM PRO 60 DELETION SEQADV 5YOZ A UNP A0A109NYM ARG 61 DELETION SEQADV 5YOZ A UNP A0A109NYM GLY 62 DELETION SEQADV 5YOZ A UNP A0A109NYM ALA 63 DELETION SEQADV 5YOZ A UNP A0A109NYM ALA 64 DELETION SEQADV 5YOZ A UNP A0A109NYM ALA 65 DELETION SEQADV 5YOZ A UNP A0A109NYM ALA 66 DELETION SEQADV 5YOZ A UNP A0A109NYM PRO 67 DELETION SEQADV 5YOZ A UNP A0A109NYM GLY 68 DELETION SEQADV 5YOZ A UNP A0A109NYM GLY 69 DELETION SEQADV 5YOZ A UNP A0A109NYM ALA 70 DELETION SEQADV 5YOZ A UNP A0A109NYM THR 71 DELETION SEQADV 5YOZ A UNP A0A109NYM SER 72 DELETION SEQADV 5YOZ A UNP A0A109NYM ALA 73 DELETION SEQADV 5YOZ A UNP A0A109NYM HIS 74 DELETION SEQADV 5YOZ A UNP A0A109NYM ALA 75 DELETION SEQADV 5YOZ A UNP A0A109NYM LEU 76 DELETION SEQADV 5YOZ A UNP A0A109NYM GLN 77 DELETION SEQADV 5YOZ A UNP A0A109NYM GLN 78 DELETION SEQADV 5YOZ A UNP A0A109NYM MET 79 DELETION SEQADV 5YOZ LEU A 72 UNP A0A109NYM GLN 92 ENGINEERED MUTATION SEQADV 5YOZ SER A 87 UNP A0A109NYM CYS 107 ENGINEERED MUTATION SEQRES 1 A 177 GLY SER MET ASN THR HIS PRO PRO GLN LEU MET GLU ALA SEQRES 2 A 177 THR SER ALA LYS ILE VAL MET LEU GLY GLU SER GLY ALA SEQRES 3 A 177 GLY LYS SER SER ILE ALA LEU ARG PHE THR ARG ASN GLU SEQRES 4 A 177 PHE LEU ALA ASN GLN GLU THR THR ILE GLY ALA ALA PHE SEQRES 5 A 177 LEU SER LYS THR VAL MET ILE ASP GLY ARG ALA LEU LYS SEQRES 6 A 177 TYR GLU ILE TRP ASP THR ALA GLY LEU GLU ARG PHE ARG SEQRES 7 A 177 SER LEU ALA PRO ILE TYR TYR ARG GLY ALA SER GLY ALA SEQRES 8 A 177 LEU VAL VAL TYR ASP ILE THR ASN SER GLU SER LEU LYS SEQRES 9 A 177 LYS ALA GLN THR TRP ILE LYS GLU LEU ARG ALA ASN ALA SEQRES 10 A 177 ASP PRO SER LEU ILE ILE VAL LEU VAL GLY ASN LYS LYS SEQRES 11 A 177 ASP LEU GLY SER LEU ARG GLN VAL SER PHE GLU ASP GLY SEQRES 12 A 177 GLN ARG LEU ALA ALA GLU GLU GLN LEU ALA ALA PHE TYR SEQRES 13 A 177 GLU ALA SER ALA LYS ASP ASN ASN ASN VAL GLU GLN VAL SEQRES 14 A 177 PHE LEU ASP LEU ALA ALA LYS LEU HELIX 1 AA1 GLY A 25 ARG A 35 1 11 HELIX 2 AA2 SER A 77 TYR A 82 1 6 HELIX 3 AA3 ASN A 97 ALA A 115 1 19 HELIX 4 AA4 LYS A 128 GLY A 131 5 4 HELIX 5 AA5 SER A 137 GLU A 148 1 12 HELIX 6 AA6 SER A 157 ASN A 161 5 5 HELIX 7 AA7 ASN A 163 LEU A 175 1 13 SHEET 1 AA1 6 ALA A 48 ILE A 57 0 SHEET 2 AA1 6 ARG A 60 THR A 69 -1 O ASP A 68 N ALA A 49 SHEET 3 AA1 6 THR A 12 LEU A 19 1 N ALA A 14 O GLU A 65 SHEET 4 AA1 6 GLY A 88 ASP A 94 1 O LEU A 90 N LEU A 19 SHEET 5 AA1 6 ILE A 120 ASN A 126 1 O VAL A 122 N ALA A 89 SHEET 6 AA1 6 ALA A 152 ALA A 156 1 O ALA A 152 N LEU A 123 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