PDB Short entry for 5LPN HEADER ENDOCYTOSIS 14-AUG-16 5LPN TITLE STRUCTURE OF HUMAN RAB10 IN COMPLEX WITH THE BMERB DOMAIN OF MICAL-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-RELATED PROTEIN RAB-10; COMPND 3 CHAIN: A, C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: PROTEIN-METHIONINE SULFOXIDE OXIDASE MICAL1; COMPND 7 CHAIN: B; COMPND 8 FRAGMENT: UNP RESIDUES 918-1067; COMPND 9 SYNONYM: MOLECULE INTERACTING WITH CASL PROTEIN 1,MICAL-1,NEDD9- COMPND 10 INTERACTING PROTEIN WITH CALPONIN HOMOLOGY AND LIM DOMAINS; COMPND 11 EC: 1.14.13.-; COMPND 12 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: RAB10; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: MICAL1, MICAL, NICAL; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MICAL-1, DUF3585, MICAL, RAB EFFECTOR, RAB10, OXIDOREDUCTASE, KEYWDS 2 ENDOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR A.RAI,A.OPRISKO,J.CAMPOS,Y.FU,T.FRIESE,A.ITZEN,R.S.GOODY,M.P.MUELLER, AUTHOR 2 E.M.GAZDAG REVDAT 5 10-JAN-24 5LPN 1 LINK REVDAT 4 06-SEP-17 5LPN 1 REMARK REVDAT 3 14-SEP-16 5LPN 1 JRNL REVDAT 2 07-SEP-16 5LPN 1 JRNL REVDAT 1 24-AUG-16 5LPN 0 JRNL AUTH A.RAI,A.OPRISKO,J.CAMPOS,Y.FU,T.FRIESE,A.ITZEN,R.S.GOODY, JRNL AUTH 2 E.M.GAZDAG,M.P.MULLER JRNL TITL BMERB DOMAINS ARE BIVALENT RAB8 FAMILY EFFECTORS EVOLVED BY JRNL TITL 2 GENE DUPLICATION. JRNL REF ELIFE V. 5 2016 JRNL REFN ESSN 2050-084X JRNL PMID 27552051 JRNL DOI 10.7554/ELIFE.18675 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 17499 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 875 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 44.0098 - 5.0859 1.00 2948 156 0.2306 0.2546 REMARK 3 2 5.0859 - 4.0377 1.00 2792 147 0.2153 0.2747 REMARK 3 3 4.0377 - 3.5276 1.00 2757 145 0.2508 0.2762 REMARK 3 4 3.5276 - 3.2051 0.99 2709 141 0.2692 0.3281 REMARK 3 5 3.2051 - 2.9755 0.99 2713 143 0.2927 0.3729 REMARK 3 6 2.9755 - 2.8001 0.99 2705 143 0.3052 0.3662 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.750 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 3793 REMARK 3 ANGLE : 1.118 5125 REMARK 3 CHIRALITY : 0.060 589 REMARK 3 PLANARITY : 0.006 644 REMARK 3 DIHEDRAL : 20.515 2282 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 1.7086 73.9068 216.9504 REMARK 3 T TENSOR REMARK 3 T11: 0.3390 T22: 0.3542 REMARK 3 T33: 0.3078 T12: 0.0622 REMARK 3 T13: -0.0207 T23: -0.0427 REMARK 3 L TENSOR REMARK 3 L11: 0.7826 L22: 0.7247 REMARK 3 L33: 1.0177 L12: -0.5522 REMARK 3 L13: 0.2051 L23: -0.6177 REMARK 3 S TENSOR REMARK 3 S11: -0.0376 S12: -0.2198 S13: -0.1146 REMARK 3 S21: 0.2532 S22: 0.1731 S23: -0.0524 REMARK 3 S31: -0.2518 S32: -0.1436 S33: 0.0247 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 5LPN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1200001091. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.6-8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99997 REMARK 200 MONOCHROMATOR : SI(111) 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17508 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 44.004 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.70 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : 0.12300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.60 REMARK 200 R MERGE FOR SHELL (I) : 0.72300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.250 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4LHW AND 5SZG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6%-10% PEG8000 0.1M IMIDAZOLE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 29.19500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 99.09000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 99.09000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 29.19500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.50000 REMARK 290 SMTRY3 4 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 GLY A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 LYS A 4 REMARK 465 GLY B 915 REMARK 465 HIS B 916 REMARK 465 MET B 917 REMARK 465 MET B 1015 REMARK 465 ASN B 1016 REMARK 465 ARG B 1017 REMARK 465 GLU B 1018 REMARK 465 GLU B 1019 REMARK 465 ASN B 1020 REMARK 465 LEU B 1021 REMARK 465 LYS B 1022 REMARK 465 THR B 1023 REMARK 465 ALA B 1024 REMARK 465 ALA B 1025 REMARK 465 LEU B 1061 REMARK 465 GLY B 1062 REMARK 465 THR B 1063 REMARK 465 GLY B 1064 REMARK 465 ALA B 1065 REMARK 465 GLN B 1066 REMARK 465 GLY B 1067 REMARK 465 GLY C -1 REMARK 465 HIS C 0 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 LYS C 3 REMARK 465 LYS C 4 REMARK 465 THR C 5 REMARK 465 ARG C 147 REMARK 465 PHE C 148 REMARK 465 PHE C 149 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 54 CG CD OE1 NE2 REMARK 470 ARG A 80 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 918 CG CD CE NZ REMARK 470 GLU B 919 CG CD OE1 OE2 REMARK 470 GLU B 920 CG CD OE1 OE2 REMARK 470 GLU B 921 CG CD OE1 OE2 REMARK 470 MET B 922 CG SD CE REMARK 470 LYS B 923 CG CD CE NZ REMARK 470 ARG B 924 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 925 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS B 927 CG CD CE NZ REMARK 470 LYS B 951 CG CD CE NZ REMARK 470 LEU B 974 CG CD1 CD2 REMARK 470 LYS B 980 CG CD CE NZ REMARK 470 ASP B1026 CG OD1 OD2 REMARK 470 ARG B1027 CG CD NE CZ NH1 NH2 REMARK 470 GLN B1028 CG CD OE1 NE2 REMARK 470 GLN B1032 CG CD OE1 NE2 REMARK 470 LYS B1036 CG CD CE NZ REMARK 470 GLU B1058 CG CD OE1 OE2 REMARK 470 ARG C 28 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 56 CG CD CE NZ REMARK 470 ARG C 80 CG CD NE CZ NH1 NH2 REMARK 470 ASP C 108 CG OD1 OD2 REMARK 470 GLU C 113 CG CD OE1 OE2 REMARK 470 ASP C 114 CG OD1 OD2 REMARK 470 ARG C 142 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 172 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 173 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 C 95 OE2 GLU C 98 1.43 REMARK 500 O LYS C 95 CD GLU C 98 1.86 REMARK 500 OD1 ASP A 17 NE1 TRP A 103 2.08 REMARK 500 NH1 ARG A 130 O VAL A 132 2.12 REMARK 500 CD1 TYR C 89 CE2 PHE C 97 2.14 REMARK 500 O PHE A 29 NZ LYS A 49 2.15 REMARK 500 O LEU A 171 OG1 THR A 174 2.16 REMARK 500 OE1 GLN A 68 N ARG A 70 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 105 NE ARG A 105 CZ -0.089 REMARK 500 ARG A 105 CZ ARG A 105 NH1 -0.092 REMARK 500 TRP C 103 CB TRP C 103 CG -0.135 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU B 956 CB - CG - CD1 ANGL. DEV. = -12.6 DEGREES REMARK 500 TYR C 89 CB - CG - CD1 ANGL. DEV. = -5.1 DEGREES 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 LYS A 123 44.93 70.23 REMARK 500 LYS A 173 37.70 -97.01 REMARK 500 ALA B 955 -38.42 -38.49 REMARK 500 THR C 73 -71.76 -60.21 REMARK 500 ASN C 158 16.60 47.75 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 MG A 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 23 OG1 REMARK 620 2 THR A 41 OG1 99.3 REMARK 620 3 GNP A 202 O3G 147.5 95.9 REMARK 620 4 GNP A 202 O2B 78.7 172.5 82.4 REMARK 620 5 HOH A 301 O 74.3 96.4 75.6 76.1 REMARK 620 6 HOH A 302 O 101.7 121.2 94.5 66.2 142.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR C 23 OG1 REMARK 620 2 THR C 41 OG1 83.7 REMARK 620 3 GNP C 202 O2G 152.4 100.3 REMARK 620 4 GNP C 202 O1B 90.4 160.0 76.5 REMARK 620 5 HOH C 301 O 111.9 109.0 92.8 90.9 REMARK 620 6 HOH C 302 O 75.1 91.4 77.5 68.6 158.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP C 202 DBREF 5LPN A 1 175 UNP P61026 RAB10_HUMAN 1 175 DBREF 5LPN B 918 1067 UNP Q8TDZ2 MICA1_HUMAN 918 1067 DBREF 5LPN C 1 175 UNP P61026 RAB10_HUMAN 1 175 SEQADV 5LPN GLY A -1 UNP P61026 EXPRESSION TAG SEQADV 5LPN HIS A 0 UNP P61026 EXPRESSION TAG SEQADV 5LPN GLY B 915 UNP Q8TDZ2 EXPRESSION TAG SEQADV 5LPN HIS B 916 UNP Q8TDZ2 EXPRESSION TAG SEQADV 5LPN MET B 917 UNP Q8TDZ2 EXPRESSION TAG SEQADV 5LPN GLY C -1 UNP P61026 EXPRESSION TAG SEQADV 5LPN HIS C 0 UNP P61026 EXPRESSION TAG SEQRES 1 A 177 GLY HIS MET ALA LYS LYS THR TYR ASP LEU LEU PHE LYS SEQRES 2 A 177 LEU LEU LEU ILE GLY ASP SER GLY VAL GLY LYS THR CYS SEQRES 3 A 177 VAL LEU PHE ARG PHE SER ASP ASP ALA PHE ASN THR THR SEQRES 4 A 177 PHE ILE SER THR ILE GLY ILE ASP PHE LYS ILE LYS THR SEQRES 5 A 177 VAL GLU LEU GLN GLY LYS LYS ILE LYS LEU GLN ILE TRP SEQRES 6 A 177 ASP THR ALA GLY GLN GLU ARG PHE HIS THR ILE THR THR SEQRES 7 A 177 SER TYR TYR ARG GLY ALA MET GLY ILE MET LEU VAL TYR SEQRES 8 A 177 ASP ILE THR ASN GLY LYS SER PHE GLU ASN ILE SER LYS SEQRES 9 A 177 TRP LEU ARG ASN ILE ASP GLU HIS ALA ASN GLU ASP VAL SEQRES 10 A 177 GLU ARG MET LEU LEU GLY ASN LYS CYS ASP MET ASP ASP SEQRES 11 A 177 LYS ARG VAL VAL PRO LYS GLY LYS GLY GLU GLN ILE ALA SEQRES 12 A 177 ARG GLU HIS GLY ILE ARG PHE PHE GLU THR SER ALA LYS SEQRES 13 A 177 ALA ASN ILE ASN ILE GLU LYS ALA PHE LEU THR LEU ALA SEQRES 14 A 177 GLU ASP ILE LEU ARG LYS THR PRO SEQRES 1 B 153 GLY HIS MET LYS GLU GLU GLU MET LYS ARG PHE CYS LYS SEQRES 2 B 153 ALA GLN THR ILE GLN ARG ARG LEU ASN GLU ILE GLU ALA SEQRES 3 B 153 ALA LEU ARG GLU LEU GLU ALA GLU GLY VAL LYS LEU GLU SEQRES 4 B 153 LEU ALA LEU ARG ARG GLN SER SER SER PRO GLU GLN GLN SEQRES 5 B 153 LYS LYS LEU TRP VAL GLY GLN LEU LEU GLN LEU VAL ASP SEQRES 6 B 153 LYS LYS ASN SER LEU VAL ALA GLU GLU ALA GLU LEU MET SEQRES 7 B 153 ILE THR VAL GLN GLU LEU ASN LEU GLU GLU LYS GLN TRP SEQRES 8 B 153 GLN LEU ASP GLN GLU LEU ARG GLY TYR MET ASN ARG GLU SEQRES 9 B 153 GLU ASN LEU LYS THR ALA ALA ASP ARG GLN ALA GLU ASP SEQRES 10 B 153 GLN VAL LEU ARG LYS LEU VAL ASP LEU VAL ASN GLN ARG SEQRES 11 B 153 ASP ALA LEU ILE ARG PHE GLN GLU GLU ARG ARG LEU SER SEQRES 12 B 153 GLU LEU ALA LEU GLY THR GLY ALA GLN GLY SEQRES 1 C 177 GLY HIS MET ALA LYS LYS THR TYR ASP LEU LEU PHE LYS SEQRES 2 C 177 LEU LEU LEU ILE GLY ASP SER GLY VAL GLY LYS THR CYS SEQRES 3 C 177 VAL LEU PHE ARG PHE SER ASP ASP ALA PHE ASN THR THR SEQRES 4 C 177 PHE ILE SER THR ILE GLY ILE ASP PHE LYS ILE LYS THR SEQRES 5 C 177 VAL GLU LEU GLN GLY LYS LYS ILE LYS LEU GLN ILE TRP SEQRES 6 C 177 ASP THR ALA GLY GLN GLU ARG PHE HIS THR ILE THR THR SEQRES 7 C 177 SER TYR TYR ARG GLY ALA MET GLY ILE MET LEU VAL TYR SEQRES 8 C 177 ASP ILE THR ASN GLY LYS SER PHE GLU ASN ILE SER LYS SEQRES 9 C 177 TRP LEU ARG ASN ILE ASP GLU HIS ALA ASN GLU ASP VAL SEQRES 10 C 177 GLU ARG MET LEU LEU GLY ASN LYS CYS ASP MET ASP ASP SEQRES 11 C 177 LYS ARG VAL VAL PRO LYS GLY LYS GLY GLU GLN ILE ALA SEQRES 12 C 177 ARG GLU HIS GLY ILE ARG PHE PHE GLU THR SER ALA LYS SEQRES 13 C 177 ALA ASN ILE ASN ILE GLU LYS ALA PHE LEU THR LEU ALA SEQRES 14 C 177 GLU ASP ILE LEU ARG LYS THR PRO HET MG A 201 1 HET GNP A 202 32 HET MG C 201 1 HET GNP C 202 32 HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER FORMUL 4 MG 2(MG 2+) FORMUL 5 GNP 2(C10 H17 N6 O13 P3) FORMUL 8 HOH *4(H2 O) HELIX 1 AA1 GLY A 21 ASP A 32 1 12 HELIX 2 AA2 GLN A 68 ARG A 70 5 3 HELIX 3 AA3 PHE A 71 SER A 77 1 7 HELIX 4 AA4 TYR A 78 ALA A 82 5 5 HELIX 5 AA5 ASN A 93 ASN A 99 1 7 HELIX 6 AA6 ASN A 99 ALA A 111 1 13 HELIX 7 AA7 PRO A 133 GLY A 145 1 13 HELIX 8 AA8 ASN A 158 LYS A 173 1 16 HELIX 9 AA9 GLU B 919 SER B 960 1 42 HELIX 10 AB1 SER B 962 GLN B 973 1 12 HELIX 11 AB2 GLN B 973 TYR B 1014 1 42 HELIX 12 AB3 ARG B 1027 ALA B 1060 1 34 HELIX 13 AB4 GLY C 21 ASP C 32 1 12 HELIX 14 AB5 GLU C 52 LYS C 56 5 5 HELIX 15 AB6 GLN C 68 ARG C 80 5 13 HELIX 16 AB7 ASN C 99 ALA C 111 1 13 HELIX 17 AB8 PRO C 133 GLY C 145 1 13 HELIX 18 AB9 ASN C 158 ARG C 172 1 15 SHEET 1 AA1 6 ILE A 44 LEU A 53 0 SHEET 2 AA1 6 LYS A 56 THR A 65 -1 O LYS A 56 N LEU A 53 SHEET 3 AA1 6 LEU A 8 GLY A 16 1 N LEU A 8 O LYS A 59 SHEET 4 AA1 6 GLY A 84 ASP A 90 1 O MET A 86 N LEU A 13 SHEET 5 AA1 6 GLU A 116 ASN A 122 1 O LEU A 120 N LEU A 87 SHEET 6 AA1 6 ARG A 147 THR A 151 1 O PHE A 149 N GLY A 121 SHEET 1 AA2 5 ILE C 44 VAL C 51 0 SHEET 2 AA2 5 ILE C 58 THR C 65 -1 O ILE C 58 N VAL C 51 SHEET 3 AA2 5 LEU C 8 ILE C 15 1 N LEU C 12 O TRP C 63 SHEET 4 AA2 5 GLY C 84 ASP C 90 1 O VAL C 88 N ILE C 15 SHEET 5 AA2 5 MET C 118 ASN C 122 1 O ASN C 122 N TYR C 89 LINK OG1 THR A 23 MG MG A 201 1555 1555 1.94 LINK OG1 THR A 41 MG MG A 201 1555 1555 1.99 LINK MG MG A 201 O3G GNP A 202 1555 1555 1.93 LINK MG MG A 201 O2B GNP A 202 1555 1555 2.38 LINK MG MG A 201 O HOH A 301 1555 1555 2.12 LINK MG MG A 201 O HOH A 302 1555 1555 1.94 LINK OG1 THR C 23 MG MG C 201 1555 1555 1.98 LINK OG1 THR C 41 MG MG C 201 1555 1555 2.00 LINK MG MG C 201 O2G GNP C 202 1555 1555 1.92 LINK MG MG C 201 O1B GNP C 202 1555 1555 2.39 LINK MG MG C 201 O HOH C 301 1555 1555 2.39 LINK MG MG C 201 O HOH C 302 1555 1555 2.01 SITE 1 AC1 6 THR A 23 THR A 41 ASP A 64 GNP A 202 SITE 2 AC1 6 HOH A 301 HOH A 302 SITE 1 AC2 25 ASP A 17 SER A 18 GLY A 19 VAL A 20 SITE 2 AC2 25 GLY A 21 LYS A 22 THR A 23 CYS A 24 SITE 3 AC2 25 PHE A 34 ASN A 35 THR A 36 PHE A 38 SITE 4 AC2 25 SER A 40 THR A 41 GLY A 67 ASN A 122 SITE 5 AC2 25 LYS A 123 ASP A 125 MET A 126 SER A 152 SITE 6 AC2 25 ALA A 153 LYS A 154 MG A 201 HOH A 301 SITE 7 AC2 25 HOH A 302 SITE 1 AC3 5 THR C 23 THR C 41 GNP C 202 HOH C 301 SITE 2 AC3 5 HOH C 302 SITE 1 AC4 24 ASP C 17 SER C 18 GLY C 19 VAL C 20 SITE 2 AC4 24 GLY C 21 LYS C 22 THR C 23 CYS C 24 SITE 3 AC4 24 PHE C 34 ASN C 35 THR C 36 PHE C 38 SITE 4 AC4 24 THR C 41 GLY C 67 ASN C 122 LYS C 123 SITE 5 AC4 24 ASP C 125 MET C 126 SER C 152 ALA C 153 SITE 6 AC4 24 LYS C 154 MG C 201 HOH C 301 HOH C 302 CRYST1 58.390 59.000 198.180 90.00 90.00 90.00 P 21 21 21 8 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 0.017126 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016949 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005046 0.00000