HEADER HYDROLASE 20-AUG-04 1X9D TITLE CRYSTAL STRUCTURE OF HUMAN CLASS I ALPHA-1,2-MANNOSIDASE IN COMPLEX TITLE 2 WITH THIO-DISACCHARIDE SUBSTRATE ANALOGUE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOPLASMIC RETICULUM MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA- COMPND 3 MANNOSIDASE; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: RESIDUES 243-699; COMPND 6 SYNONYM: ER ALPHA-1,2-MANNOSIDASE, MANNOSIDASE ALPHA CLASS 1B MEMBER COMPND 7 1, MAN9GLCNAC2-SPECIFIC PROCESSING ALPHA-MANNOSIDASE, UNQ747/PRO1477; COMPND 8 EC: 3.2.1.113; COMPND 9 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: MAN1B1; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS MANNOSIDASE, SUBSTRATE ANALOGUE, GLYCOSYL HYDROLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.KARAVEG,W.TEMPEL,Z.J.LIU,A.SIRIWARDENA,K.W.MOREMEN,B.C.WANG REVDAT 6 23-AUG-23 1X9D 1 HETSYN REVDAT 5 29-JUL-20 1X9D 1 COMPND REMARK SEQADV HET REVDAT 5 2 1 HETNAM FORMUL LINK SITE REVDAT 5 3 1 ATOM REVDAT 4 11-OCT-17 1X9D 1 REMARK REVDAT 3 24-FEB-09 1X9D 1 VERSN REVDAT 2 27-SEP-05 1X9D 1 JRNL REMARK REVDAT 1 22-FEB-05 1X9D 0 JRNL AUTH K.KARAVEG,A.SIRIWARDENA,W.TEMPEL,Z.J.LIU,J.GLUSHKA,B.C.WANG, JRNL AUTH 2 K.W.MOREMEN JRNL TITL MECHANISM OF CLASS 1 (GLYCOSYLHYDROLASE FAMILY 47) JRNL TITL 2 {ALPHA}-MANNOSIDASES INVOLVED IN N-GLYCAN PROCESSING AND JRNL TITL 3 ENDOPLASMIC RETICULUM QUALITY CONTROL. JRNL REF J.BIOL.CHEM. V. 280 16197 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15713668 JRNL DOI 10.1074/JBC.M500119200 REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REFMAC_5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 76092 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.146 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 8507 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.41 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.45 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5417 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.1580 REMARK 3 BIN FREE R VALUE SET COUNT : 631 REMARK 3 BIN FREE R VALUE : 0.1930 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3592 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 35 REMARK 3 SOLVENT ATOMS : 375 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.26000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : -0.25000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : 0.02000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.056 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.029 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.690 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3804 ; 0.014 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): 3410 ; 0.002 ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5168 ; 1.337 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): 7931 ; 0.826 ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 451 ; 5.907 ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 633 ;11.599 ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 572 ; 0.087 ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4162 ; 0.005 ; NULL REMARK 3 GENERAL PLANES OTHERS (A): 801 ; 0.001 ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 774 ; 0.220 ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3444 ; 0.167 ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2001 ; 0.082 ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 294 ; 0.095 ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 4 ; 0.155 ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): 40 ; 0.240 ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.069 ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2309 ; 1.717 ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3664 ; 2.257 ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1689 ; 2.439 ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1504 ; 3.505 ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1X9D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-SEP-04. REMARK 100 THE DEPOSITION ID IS D_1000030103. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99985 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84600 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.12900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1FMI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 4000, 50MM AMMONIUM SULFATE, REMARK 280 0.1M MES, 10% 1,4-BUTANEDIOL, PH 6.5, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLU A 162 REMARK 465 PHE A 163 REMARK 465 ALA A 164 REMARK 465 LEU A 165 REMARK 465 LEU A 166 REMARK 465 THR A 167 REMARK 465 CYS A 168 REMARK 465 ARG A 169 REMARK 465 LEU A 170 REMARK 465 ASP A 171 REMARK 465 PRO A 172 REMARK 465 PRO A 173 REMARK 465 SER A 174 REMARK 465 GLN A 175 REMARK 465 ASP A 176 REMARK 465 LEU A 177 REMARK 465 LYS A 178 REMARK 465 ASP A 179 REMARK 465 GLY A 180 REMARK 465 THR A 181 REMARK 465 GLN A 182 REMARK 465 GLU A 183 REMARK 465 GLU A 184 REMARK 465 ALA A 185 REMARK 465 THR A 186 REMARK 465 LYS A 187 REMARK 465 ARG A 188 REMARK 465 GLN A 189 REMARK 465 GLU A 190 REMARK 465 ALA A 191 REMARK 465 PRO A 192 REMARK 465 VAL A 193 REMARK 465 ASP A 194 REMARK 465 PRO A 195 REMARK 465 ARG A 196 REMARK 465 PRO A 197 REMARK 465 GLU A 198 REMARK 465 GLY A 199 REMARK 465 ASP A 200 REMARK 465 PRO A 201 REMARK 465 GLN A 202 REMARK 465 ARG A 203 REMARK 465 THR A 204 REMARK 465 VAL A 205 REMARK 465 ILE A 206 REMARK 465 SER A 207 REMARK 465 TRP A 208 REMARK 465 ARG A 209 REMARK 465 GLY A 210 REMARK 465 ALA A 211 REMARK 465 VAL A 212 REMARK 465 ILE A 213 REMARK 465 GLU A 214 REMARK 465 PRO A 215 REMARK 465 GLU A 216 REMARK 465 GLN A 217 REMARK 465 GLY A 218 REMARK 465 THR A 219 REMARK 465 GLU A 220 REMARK 465 LEU A 221 REMARK 465 PRO A 222 REMARK 465 SER A 223 REMARK 465 ARG A 224 REMARK 465 ARG A 225 REMARK 465 ALA A 226 REMARK 465 GLU A 227 REMARK 465 VAL A 228 REMARK 465 PRO A 229 REMARK 465 THR A 230 REMARK 465 LYS A 231 REMARK 465 PRO A 232 REMARK 465 PRO A 233 REMARK 465 LEU A 234 REMARK 465 PRO A 235 REMARK 465 PRO A 236 REMARK 465 ALA A 237 REMARK 465 ARG A 238 REMARK 465 THR A 239 REMARK 465 GLN A 240 REMARK 465 GLY A 241 REMARK 465 THR A 242 REMARK 465 PRO A 243 REMARK 465 VAL A 244 REMARK 465 PRO A 676 REMARK 465 PRO A 698 REMARK 465 ALA A 699 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 HIS A 245 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 312 CD CE NZ REMARK 470 LYS A 316 CG CD CE NZ REMARK 470 LYS A 322 CG CD CE NZ REMARK 470 ARG A 367 CD NE CZ NH1 NH2 REMARK 470 LYS A 371 CE NZ REMARK 470 ARG A 388 CB CG CD NE CZ NH1 NH2 REMARK 470 TRP A 389 CB CG CD1 CD2 NE1 CE2 CE3 REMARK 470 TRP A 389 CZ2 CZ3 CH2 REMARK 470 LYS A 415 CG CD CE NZ REMARK 470 LYS A 423 NZ REMARK 470 ARG A 461 CZ NH1 NH2 REMARK 470 ARG A 517 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 547 CD OE1 OE2 REMARK 470 ARG A 582 NE CZ NH1 NH2 REMARK 470 ARG A 583 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 629 CZ NH1 NH2 REMARK 470 GLN A 648 CD OE1 NE2 REMARK 470 LYS A 649 CD CE NZ REMARK 470 GLU A 651 CD OE1 OE2 REMARK 470 THR A 697 CA C O CB OG1 CG2 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 SER A 331 CA SER A 331 CB 0.090 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 ASP A 323 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 325 CB - CG - OD2 ANGL. DEV. = 6.0 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 ALA A 268 24.43 -144.57 REMARK 500 SER A 280 -157.43 -143.94 REMARK 500 TRP A 284 -46.99 -133.48 REMARK 500 TRP A 284 -43.14 -133.48 REMARK 500 ARG A 461 -11.77 91.51 REMARK 500 ALA A 462 -39.07 -132.84 REMARK 500 ASP A 463 -67.13 -24.43 REMARK 500 ALA A 520 38.99 -86.73 REMARK 500 GLU A 651 77.40 64.08 REMARK 500 GLU A 663 -59.27 -121.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 BU1 A 1004 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 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 688 OG1 REMARK 620 2 THR A 688 O 72.9 REMARK 620 3 HOH A1005 O 74.1 81.8 REMARK 620 4 HOH A1008 O 72.2 142.8 76.9 REMARK 620 5 HOH A1009 O 129.4 147.1 124.4 68.7 REMARK 620 6 HOH A1010 O 146.3 91.7 74.1 110.9 79.0 REMARK 620 7 MAN B 2 O2 73.1 84.2 146.9 97.5 81.4 136.3 REMARK 620 8 MAN B 2 O3 127.0 70.9 134.9 143.3 76.2 71.7 65.9 REMARK 620 N 1 2 3 4 5 6 7 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FMI RELATED DB: PDB REMARK 900 MOLECULAR REPLACEMENT MODEL OF HUMAN CLASS I 1,2-MANNOSIDASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE IS STRONG EVIDENCE FOR SPONTANEOUS N-TERMINAL REMARK 999 TRUNCATION PRIOR TO CRYSTALLIZATION. HOWEVER, THE REMARK 999 PRECISE POSITION OF THE N-TERMINUS OF THE REMARK 999 CRYSTALLIZING PEPTIDE HAS NOT BEEN DETERMINED. DBREF 1X9D A 172 699 UNP Q9UKM7 MA1B1_HUMAN 172 699 SEQADV 1X9D GLU A 162 UNP Q9UKM7 CLONING ARTIFACT SEQADV 1X9D PHE A 163 UNP Q9UKM7 CLONING ARTIFACT SEQADV 1X9D ALA A 164 UNP Q9UKM7 CLONING ARTIFACT SEQADV 1X9D LEU A 165 UNP Q9UKM7 CLONING ARTIFACT SEQADV 1X9D LEU A 166 UNP Q9UKM7 CLONING ARTIFACT SEQADV 1X9D THR A 167 UNP Q9UKM7 CLONING ARTIFACT SEQADV 1X9D CYS A 168 UNP Q9UKM7 CLONING ARTIFACT SEQADV 1X9D ARG A 169 UNP Q9UKM7 CLONING ARTIFACT SEQADV 1X9D LEU A 170 UNP Q9UKM7 CLONING ARTIFACT SEQADV 1X9D ASP A 171 UNP Q9UKM7 CLONING ARTIFACT SEQRES 1 A 538 GLU PHE ALA LEU LEU THR CYS ARG LEU ASP PRO PRO SER SEQRES 2 A 538 GLN ASP LEU LYS ASP GLY THR GLN GLU GLU ALA THR LYS SEQRES 3 A 538 ARG GLN GLU ALA PRO VAL ASP PRO ARG PRO GLU GLY ASP SEQRES 4 A 538 PRO GLN ARG THR VAL ILE SER TRP ARG GLY ALA VAL ILE SEQRES 5 A 538 GLU PRO GLU GLN GLY THR GLU LEU PRO SER ARG ARG ALA SEQRES 6 A 538 GLU VAL PRO THR LYS PRO PRO LEU PRO PRO ALA ARG THR SEQRES 7 A 538 GLN GLY THR PRO VAL HIS LEU ASN TYR ARG GLN LYS GLY SEQRES 8 A 538 VAL ILE ASP VAL PHE LEU HIS ALA TRP LYS GLY TYR ARG SEQRES 9 A 538 LYS PHE ALA TRP GLY HIS ASP GLU LEU LYS PRO VAL SER SEQRES 10 A 538 ARG SER PHE SER GLU TRP PHE GLY LEU GLY LEU THR LEU SEQRES 11 A 538 ILE ASP ALA LEU ASP THR MET TRP ILE LEU GLY LEU ARG SEQRES 12 A 538 LYS GLU PHE GLU GLU ALA ARG LYS TRP VAL SER LYS LYS SEQRES 13 A 538 LEU HIS PHE GLU LYS ASP VAL ASP VAL ASN LEU PHE GLU SEQRES 14 A 538 SER THR ILE ARG ILE LEU GLY GLY LEU LEU SER ALA TYR SEQRES 15 A 538 HIS LEU SER GLY ASP SER LEU PHE LEU ARG LYS ALA GLU SEQRES 16 A 538 ASP PHE GLY ASN ARG LEU MET PRO ALA PHE ARG THR PRO SEQRES 17 A 538 SER LYS ILE PRO TYR SER ASP VAL ASN ILE GLY THR GLY SEQRES 18 A 538 VAL ALA HIS PRO PRO ARG TRP THR SER ASP SER THR VAL SEQRES 19 A 538 ALA GLU VAL THR SER ILE GLN LEU GLU PHE ARG GLU LEU SEQRES 20 A 538 SER ARG LEU THR GLY ASP LYS LYS PHE GLN GLU ALA VAL SEQRES 21 A 538 GLU LYS VAL THR GLN HIS ILE HIS GLY LEU SER GLY LYS SEQRES 22 A 538 LYS ASP GLY LEU VAL PRO MET PHE ILE ASN THR HIS SER SEQRES 23 A 538 GLY LEU PHE THR HIS LEU GLY VAL PHE THR LEU GLY ALA SEQRES 24 A 538 ARG ALA ASP SER TYR TYR GLU TYR LEU LEU LYS GLN TRP SEQRES 25 A 538 ILE GLN GLY GLY LYS GLN GLU THR GLN LEU LEU GLU ASP SEQRES 26 A 538 TYR VAL GLU ALA ILE GLU GLY VAL ARG THR HIS LEU LEU SEQRES 27 A 538 ARG HIS SER GLU PRO SER LYS LEU THR PHE VAL GLY GLU SEQRES 28 A 538 LEU ALA HIS GLY ARG PHE SER ALA LYS MET ASP HIS LEU SEQRES 29 A 538 VAL CYS PHE LEU PRO GLY THR LEU ALA LEU GLY VAL TYR SEQRES 30 A 538 HIS GLY LEU PRO ALA SER HIS MET GLU LEU ALA GLN GLU SEQRES 31 A 538 LEU MET GLU THR CYS TYR GLN MET ASN ARG GLN MET GLU SEQRES 32 A 538 THR GLY LEU SER PRO GLU ILE VAL HIS PHE ASN LEU TYR SEQRES 33 A 538 PRO GLN PRO GLY ARG ARG ASP VAL GLU VAL LYS PRO ALA SEQRES 34 A 538 ASP ARG HIS ASN LEU LEU ARG PRO GLU THR VAL GLU SER SEQRES 35 A 538 LEU PHE TYR LEU TYR ARG VAL THR GLY ASP ARG LYS TYR SEQRES 36 A 538 GLN ASP TRP GLY TRP GLU ILE LEU GLN SER PHE SER ARG SEQRES 37 A 538 PHE THR ARG VAL PRO SER GLY GLY TYR SER SER ILE ASN SEQRES 38 A 538 ASN VAL GLN ASP PRO GLN LYS PRO GLU PRO ARG ASP LYS SEQRES 39 A 538 MET GLU SER PHE PHE LEU GLY GLU THR LEU LYS TYR LEU SEQRES 40 A 538 PHE LEU LEU PHE SER ASP ASP PRO ASN LEU LEU SER LEU SEQRES 41 A 538 ASP ALA TYR VAL PHE ASN THR GLU ALA HIS PRO LEU PRO SEQRES 42 A 538 ILE TRP THR PRO ALA HET Z5L B 1 13 HET MAN B 2 11 HET CA A1001 1 HET SO4 A1002 5 HET BU1 A1004 5 HETNAM Z5L METHYL 2-THIO-ALPHA-D-MANNOPYRANOSIDE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION HETNAM BU1 1,4-BUTANEDIOL HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE FORMUL 2 Z5L C7 H14 O5 S FORMUL 2 MAN C6 H12 O6 FORMUL 3 CA CA 2+ FORMUL 4 SO4 O4 S 2- FORMUL 5 BU1 C4 H10 O2 FORMUL 6 HOH *375(H2 O) HELIX 1 1 ASN A 247 ALA A 268 1 22 HELIX 2 2 GLY A 288 LEU A 301 1 14 HELIX 3 3 LEU A 303 LEU A 318 1 16 HELIX 4 4 LEU A 328 GLY A 347 1 20 HELIX 5 5 ASP A 348 MET A 363 1 16 HELIX 6 6 PRO A 364 ARG A 367 5 4 HELIX 7 7 VAL A 395 SER A 400 1 6 HELIX 8 8 ILE A 401 GLY A 413 1 13 HELIX 9 9 LYS A 415 GLY A 430 1 16 HELIX 10 10 ALA A 462 GLY A 476 1 15 HELIX 11 11 GLU A 480 LEU A 498 1 19 HELIX 12 12 CYS A 527 HIS A 539 1 13 HELIX 13 13 PRO A 542 GLN A 562 1 21 HELIX 14 14 LYS A 588 ARG A 592 5 5 HELIX 15 15 PRO A 598 GLY A 612 1 15 HELIX 16 16 ARG A 614 THR A 631 1 18 HELIX 17 17 SER A 658 GLU A 663 1 6 HELIX 18 18 GLU A 663 SER A 673 1 11 SHEET 1 A 2 GLU A 273 LYS A 275 0 SHEET 2 A 2 SER A 280 SER A 282 -1 O SER A 280 N LYS A 275 SHEET 1 B 3 ASP A 325 ASN A 327 0 SHEET 2 B 3 ASP A 376 ASN A 378 -1 O VAL A 377 N VAL A 326 SHEET 3 B 3 ALA A 384 HIS A 385 -1 O HIS A 385 N ASP A 376 SHEET 1 C 3 ASP A 392 THR A 394 0 SHEET 2 C 3 PHE A 442 ASN A 444 -1 O ILE A 443 N SER A 393 SHEET 3 C 3 PHE A 450 THR A 451 -1 O THR A 451 N PHE A 442 SHEET 1 D 3 VAL A 455 PHE A 456 0 SHEET 2 D 3 GLU A 512 ALA A 514 -1 O LEU A 513 N PHE A 456 SHEET 3 D 3 ARG A 517 SER A 519 -1 O SER A 519 N GLU A 512 SHEET 1 E 2 LEU A 499 HIS A 501 0 SHEET 2 E 2 THR A 508 VAL A 510 -1 O PHE A 509 N ARG A 500 SHEET 1 F 2 LYS A 521 ASP A 523 0 SHEET 2 F 2 ILE A 571 HIS A 573 -1 O VAL A 572 N MET A 522 SHEET 1 G 2 TYR A 684 PHE A 686 0 SHEET 2 G 2 PRO A 692 PRO A 694 -1 O LEU A 693 N VAL A 685 SSBOND 1 CYS A 527 CYS A 556 1555 1555 2.08 LINK S2 Z5L B 1 C1 MAN B 2 1555 1555 1.83 LINK OG1 THR A 688 CA CA A1001 1555 1555 2.46 LINK O THR A 688 CA CA A1001 1555 1555 2.44 LINK CA CA A1001 O HOH A1005 1555 1555 2.54 LINK CA CA A1001 O HOH A1008 1555 1555 2.49 LINK CA CA A1001 O HOH A1009 1555 1555 2.44 LINK CA CA A1001 O HOH A1010 1555 1555 2.38 LINK CA CA A1001 O2 MAN B 2 1555 1555 2.44 LINK CA CA A1001 O3 MAN B 2 1555 1555 2.50 CISPEP 1 GLU A 503 PRO A 504 0 4.80 CRYST1 50.687 53.878 56.234 89.49 63.60 62.61 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 0.019729 -0.010222 -0.012699 0.00000 SCALE2 0.000000 0.020904 0.005306 0.00000 SCALE3 0.000000 0.000000 0.020483 0.00000