PDB Short entry for 3TOW HEADER PROTEIN TRANSPORT 06-SEP-11 3TOW TITLE CRYSTAL STRUCTURE OF THE MABP DOMAIN OF MVB12B OF HUMAN ESCRT-I TITLE 2 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: MULTIVESICULAR BODY SUBUNIT 12B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 47-192; COMPND 5 SYNONYM: ESCRT-I COMPLEX SUBUNIT MVB12B, PROTEIN FAM125B; COMPND 6 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: C9ORF28, FAM125B, MVB12B; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSFD KEYWDS BETA PRISM, MEMBRANE BINDING DOMAIN, NEGATIVELY CHARGED MEMBRANE, KEYWDS 2 PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR E.BOURA,J.H.HURLEY REVDAT 3 28-FEB-24 3TOW 1 SEQADV REVDAT 2 27-NOV-13 3TOW 1 JRNL REVDAT 1 11-JAN-12 3TOW 0 JRNL AUTH E.BOURA,J.H.HURLEY JRNL TITL STRUCTURAL BASIS FOR MEMBRANE TARGETING BY THE JRNL TITL 2 MVB12-ASSOCIATED BETA-PRISM DOMAIN OF THE HUMAN ESCRT-I JRNL TITL 3 MVB12 SUBUNIT. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 1901 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22232651 JRNL DOI 10.1073/PNAS.1117597109 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.4_486) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 27073 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1357 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 29.5370 - 2.8856 1.00 2841 149 0.1670 0.1752 REMARK 3 2 2.8856 - 2.2907 1.00 2707 146 0.1609 0.2075 REMARK 3 3 2.2907 - 2.0012 1.00 2681 142 0.1450 0.1988 REMARK 3 4 2.0012 - 1.8183 0.99 2628 148 0.1452 0.1745 REMARK 3 5 1.8183 - 1.6880 0.99 2638 135 0.1618 0.2044 REMARK 3 6 1.6880 - 1.5884 0.98 2578 139 0.1648 0.1979 REMARK 3 7 1.5884 - 1.5089 0.96 2527 129 0.1717 0.1752 REMARK 3 8 1.5089 - 1.4432 0.94 2486 137 0.1908 0.2375 REMARK 3 9 1.4432 - 1.3877 0.92 2402 131 0.2093 0.2229 REMARK 3 10 1.3877 - 1.3400 0.85 2228 101 0.2438 0.2652 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 0.40 REMARK 3 SHRINKAGE RADIUS : 0.17 REMARK 3 K_SOL : 0.51 REMARK 3 B_SOL : 57.38 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.000 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) : -0.23830 REMARK 3 B22 (A**2) : -0.01950 REMARK 3 B33 (A**2) : 0.25780 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 : 0.014 1254 REMARK 3 ANGLE : 1.465 1700 REMARK 3 CHIRALITY : 0.090 189 REMARK 3 PLANARITY : 0.007 218 REMARK 3 DIHEDRAL : 12.197 469 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3TOW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000067739. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-AUG-11; 09-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 22-ID; 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1; 0.9792, 0.9798, 0.9546 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL; SI 111 CHANNEL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD; MARMOSAIC REMARK 200 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27812 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 29.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : 0.07900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.52000 REMARK 200 R SYM FOR SHELL (I) : 0.52000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.017 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 33% PEG 400, 0.1M TRIS PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 16.18550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.69400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.30350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.69400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.18550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.30350 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 HOH A 255 O HOH A 259 1.93 REMARK 500 O HOH A 406 O HOH A 416 1.94 REMARK 500 O HOH A 246 O HOH A 411 2.00 REMARK 500 O HOH A 267 O HOH A 268 2.03 REMARK 500 O HOH A 271 O HOH A 408 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 252 O HOH A 253 4455 1.90 REMARK 500 O HOH A 249 O HOH A 250 3544 2.00 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 143 -44.89 71.92 REMARK 500 REMARK 500 REMARK: NULL DBREF 3TOW A 47 192 UNP Q9H7P6 F125B_HUMAN 47 192 SEQADV 3TOW HIS A 193 UNP Q9H7P6 EXPRESSION TAG SEQADV 3TOW HIS A 194 UNP Q9H7P6 EXPRESSION TAG SEQADV 3TOW HIS A 195 UNP Q9H7P6 EXPRESSION TAG SEQADV 3TOW HIS A 196 UNP Q9H7P6 EXPRESSION TAG SEQADV 3TOW HIS A 197 UNP Q9H7P6 EXPRESSION TAG SEQADV 3TOW HIS A 198 UNP Q9H7P6 EXPRESSION TAG SEQRES 1 A 152 MET ASP PRO ILE THR GLY VAL GLY VAL VAL ALA SER ARG SEQRES 2 A 152 ASN ARG ALA PRO THR GLY TYR ASP VAL VAL ALA GLN THR SEQRES 3 A 152 ALA ASP GLY VAL ASP ALA ASP LEU TRP LYS ASP GLY LEU SEQRES 4 A 152 PHE LYS SER LYS VAL THR ARG TYR LEU CYS PHE THR ARG SEQRES 5 A 152 SER PHE SER LYS GLU ASN SER HIS LEU GLY ASN VAL LEU SEQRES 6 A 152 VAL ASP MET LYS LEU ILE ASP ILE LYS ASP THR LEU PRO SEQRES 7 A 152 VAL GLY PHE ILE PRO ILE GLN GLU THR VAL ASP THR GLN SEQRES 8 A 152 GLU VAL ALA PHE ARG LYS LYS ARG LEU CYS ILE LYS PHE SEQRES 9 A 152 ILE PRO ARG ASP SER THR GLU ALA ALA ILE CYS ASP ILE SEQRES 10 A 152 ARG ILE MET GLY ARG THR LYS GLN ALA PRO PRO GLN TYR SEQRES 11 A 152 THR PHE ILE GLY GLU LEU ASN SER MET GLY ILE TRP TYR SEQRES 12 A 152 ARG MET GLY HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *225(H2 O) HELIX 1 1 ASN A 104 LEU A 107 5 4 HELIX 2 2 ASP A 154 THR A 156 5 3 SHEET 1 A 3 GLY A 52 VAL A 56 0 SHEET 2 A 3 TYR A 93 THR A 97 -1 O TYR A 93 N VAL A 56 SHEET 3 A 3 ASP A 67 VAL A 68 -1 N ASP A 67 O PHE A 96 SHEET 1 B 3 ASN A 109 ASP A 118 0 SHEET 2 B 3 LYS A 144 PRO A 152 -1 O LYS A 149 N VAL A 112 SHEET 3 B 3 ILE A 128 PRO A 129 -1 N ILE A 128 O ILE A 148 SHEET 1 C 3 ALA A 159 GLY A 167 0 SHEET 2 C 3 MET A 185 GLY A 192 -1 O GLY A 186 N MET A 166 SHEET 3 C 3 TYR A 176 LEU A 182 -1 N ILE A 179 O ILE A 187 CRYST1 32.371 52.607 71.388 90.00 90.00 90.00 P 21 21 21 4 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 0.030892 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019009 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014008 0.00000