HEADER TRANSPORT PROTEIN 11-JUN-15 5A4R TITLE CRYSTAL STRUCTURE OF A VITAMIN B12 TRAFFICKING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA TYPE D HOMOLOG, COMPND 3 MITOCHONDRIAL; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RESIDUES 129-296; COMPND 6 SYNONYM: MMADHC; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.KOPEC,F.FITZPATRICK,D.S.FROESE,S.VELUPILLAI,R.NOWAK,R.CHALK, AUTHOR 2 N.BURGESS-BROWN,F.VON DELFT,C.ARROWSMITH,A.EDWARDS,C.BOUNTRA, AUTHOR 3 B.FOWLER,M.R.BAUMGARTNER,W.W.YUE REVDAT 4 08-MAY-24 5A4R 1 REMARK REVDAT 3 16-DEC-15 5A4R 1 JRNL REVDAT 2 04-NOV-15 5A4R 1 JRNL REVDAT 1 28-OCT-15 5A4R 0 JRNL AUTH D.S.FROESE,J.KOPEC,F.FITZPATRICK,M.SCHULLER,T.J.MCCORVIE, JRNL AUTH 2 R.CHALK,T.PLESSL,V.FETTELSCHOSS,B.FOWLER,M.R.BAUMGARTNER, JRNL AUTH 3 W.W.YUE JRNL TITL STRUCTURAL INSIGHTS INTO THE MMACHC-MMADHC PROTEIN COMPLEX JRNL TITL 2 INVOLVED IN VITAMIN B12 TRAFFICKING. JRNL REF J.BIOL.CHEM. V. 290 29167 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 26483544 JRNL DOI 10.1074/JBC.M115.683268 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 10518 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 529 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 44.7738 - 3.5713 1.00 2582 146 0.2088 0.2303 REMARK 3 2 3.5713 - 2.8348 1.00 2494 125 0.2548 0.2873 REMARK 3 3 2.8348 - 2.4765 1.00 2471 123 0.2612 0.2956 REMARK 3 4 2.4765 - 2.2501 1.00 2442 135 0.2636 0.3254 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.00 REMARK 3 B_SOL : 0.00 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 66.20 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 : 0.007 1136 REMARK 3 ANGLE : 0.969 1539 REMARK 3 CHIRALITY : 0.037 181 REMARK 3 PLANARITY : 0.005 196 REMARK 3 DIHEDRAL : 14.461 395 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: MISSING ELECTRON DENSITY FOR RESIDUES REMARK 3 129 TO 131, 160 TO 168, 237 TO 245 REMARK 4 REMARK 4 5A4R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1290064022. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97826 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10530 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 44.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.02000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 31.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 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: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% POLYACRYLIC ACID 5100, 0.02M REMARK 280 MAGNESIUM CHLORIDE, 0.1M HEPES PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.33500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.33500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 37.10500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.76500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 37.10500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.76500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 32.33500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 37.10500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.76500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 32.33500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 37.10500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.76500 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.4 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 97.00500 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 SER A 127 REMARK 465 MET A 128 REMARK 465 PRO A 129 REMARK 465 VAL A 130 REMARK 465 GLU A 131 REMARK 465 ASP A 160 REMARK 465 PHE A 161 REMARK 465 GLU A 162 REMARK 465 SER A 163 REMARK 465 LEU A 164 REMARK 465 PHE A 165 REMARK 465 PRO A 166 REMARK 465 GLU A 167 REMARK 465 TYR A 237 REMARK 465 THR A 238 REMARK 465 ASN A 239 REMARK 465 ASN A 240 REMARK 465 THR A 241 REMARK 465 LEU A 242 REMARK 465 PHE A 243 REMARK 465 GLU A 244 REMARK 465 THR A 245 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 132 CD OE1 NE2 REMARK 470 LYS A 145 CE NZ REMARK 470 ARG A 158 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 159 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 172 CD CE NZ REMARK 470 TRP A 189 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 189 CZ3 CH2 REMARK 470 GLU A 191 CG CD OE1 OE2 REMARK 470 ASP A 246 CG OD1 OD2 REMARK 470 GLU A 247 CG CD OE1 OE2 REMARK 470 ARG A 248 CD NE CZ NH1 NH2 REMARK 470 LYS A 263 CE NZ 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 ALA A 169 -63.78 -128.34 REMARK 500 ASN A 170 74.79 58.66 REMARK 500 GLU A 247 -16.53 67.95 REMARK 500 REMARK 500 REMARK: NULL DBREF 5A4R A 129 296 UNP Q99LS1 MMAD_MOUSE 129 296 SEQADV 5A4R SER A 127 UNP Q99LS1 EXPRESSION TAG SEQADV 5A4R MET A 128 UNP Q99LS1 EXPRESSION TAG SEQRES 1 A 170 SER MET PRO VAL GLU GLN GLU ILE ASN SER ALA GLU THR SEQRES 2 A 170 TYR PHE GLU SER ALA LYS VAL GLU CYS ALA ILE GLN THR SEQRES 3 A 170 CYS PRO GLU LEU LEU ARG ARG ASP PHE GLU SER LEU PHE SEQRES 4 A 170 PRO GLU VAL ALA ASN SER LYS LEU MET ILE LEU THR VAL SEQRES 5 A 170 THR GLN LYS THR GLU ASN ASP MET THR VAL TRP SER GLU SEQRES 6 A 170 GLU VAL GLU VAL GLU ARG GLU VAL LEU LEU GLU LYS PHE SEQRES 7 A 170 ILE SER GLY ALA LYS GLU ILE CYS TYR ALA LEU ARG ALA SEQRES 8 A 170 GLU GLY TYR TRP ALA ASP PHE ILE ASP PRO SER SER GLY SEQRES 9 A 170 VAL ALA PHE PHE GLY PRO TYR THR ASN ASN THR LEU PHE SEQRES 10 A 170 GLU THR ASP GLU ARG TYR ARG HIS LEU GLY PHE SER VAL SEQRES 11 A 170 ASP ASP LEU GLY CYS CYS LYS VAL ILE ARG HIS SER LEU SEQRES 12 A 170 TRP GLY THR HIS VAL VAL VAL GLY SER ILE PHE THR ASN SEQRES 13 A 170 ALA THR ALA ASP SER SER ILE MET ARG LYS LEU SER GLY SEQRES 14 A 170 ASN FORMUL 2 HOH *26(H2 O) HELIX 1 1 SER A 136 PHE A 141 5 6 HELIX 2 2 SER A 190 ALA A 217 1 28 HELIX 3 3 GLU A 247 GLY A 253 5 7 HELIX 4 4 SER A 287 SER A 294 1 8 SHEET 1 AA 4 VAL A 146 THR A 152 0 SHEET 2 AA 4 MET A 174 LYS A 181 -1 O ILE A 175 N GLN A 151 SHEET 3 AA 4 VAL A 274 THR A 281 -1 O VAL A 275 N GLN A 180 SHEET 4 AA 4 ALA A 222 PHE A 224 -1 O ASP A 223 N PHE A 280 SHEET 1 AB 2 SER A 255 ASP A 258 0 SHEET 2 AB 2 LYS A 263 ARG A 266 -1 O VAL A 264 N ASP A 257 CRYST1 74.210 89.530 64.670 90.00 90.00 90.00 C 2 2 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 0.013475 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011169 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015463 0.00000