HEADER HYDROLASE 21-JUN-12 4AYQ TITLE STRUCTURE OF THE GH47 PROCESSING ALPHA-1,2-MANNOSIDASE FROM TITLE 2 CAULOBACTER STRAIN K31 IN COMPLEX WITH MANNOIMIDAZOLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNOSYL-OLIGOSACCHARIDE 1,2-ALPHA-MANNOSIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALPHA-1\,2-MANNOSIDASE; COMPND 5 EC: 3.2.1.113; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAULOBACTER SP.; SOURCE 3 ORGANISM_TAXID: 366602; SOURCE 4 STRAIN: K31; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: TUNER; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET21A KEYWDS HYDROLASE, GLYCOSIDE HYDROLASE, GH47, CAZY, ENZYME-CARBOHYDRATE KEYWDS 2 INTERACTION, MANNOSE, GLYCOSIDASE INHIBITION, QUANTUM MECHANICS EXPDTA X-RAY DIFFRACTION AUTHOR A.J.THOMPSON,J.DABIN,J.IGLESIAS-FERNANDEZ,A.IGLESIAS-FERNANDEZ, AUTHOR 2 Z.DINEV,S.J.WILLIAMS,A.SIRIWARDENA,C.MORELAND,T.C.HU,D.K.SMITH, AUTHOR 3 H.J.GILBERT,C.ROVIRA,G.J.DAVIES REVDAT 3 01-MAY-24 4AYQ 1 REMARK LINK REVDAT 2 25-MAR-15 4AYQ 1 JRNL REVDAT 1 30-JAN-13 4AYQ 0 JRNL AUTH A.J.THOMPSON,J.DABIN,J.IGLESIAS-FERNANDEZ,A.ARDEVOL,Z.DINEV, JRNL AUTH 2 S.J.WILLIAMS,O.BANDE,A.SIRIWARDENA,C.MORELAND,T.C.HU, JRNL AUTH 3 D.K.SMITH,H.J.GILBERT,C.ROVIRA,G.J.DAVIES JRNL TITL THE REACTION COORDINATE OF A BACTERIAL GH47 JRNL TITL 2 ALPHA-MANNOSIDASE: A COMBINED QUANTUM MECHANICAL AND JRNL TITL 3 STRUCTURAL APPROACH. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 51 10997 2012 JRNL REFN ISSN 1433-7851 JRNL PMID 23012075 JRNL DOI 10.1002/ANIE.201205338 REMARK 2 REMARK 2 RESOLUTION. 1.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0025 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 147134 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) : 0.089 REMARK 3 R VALUE (WORKING SET) : 0.088 REMARK 3 FREE R VALUE : 0.105 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7772 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) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9814 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.1460 REMARK 3 BIN FREE R VALUE SET COUNT : 480 REMARK 3 BIN FREE R VALUE : 0.1690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3451 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 827 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.01000 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.020 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.021 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.011 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.500 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.987 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.983 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3715 ; 0.010 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 3457 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5063 ; 1.392 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7943 ; 0.818 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 473 ; 6.123 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 182 ;33.889 ;22.857 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 592 ;11.615 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;16.490 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 532 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4265 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 930 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1928 ; 0.273 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3525 ; 0.175 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1837 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1957 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 113 ; 0.106 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.100 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 11 ; 0.070 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 194 ; 0.306 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 62 ; 0.266 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.158 ; 0.200 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; 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): 7170 ; 1.614 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 132 ;38.456 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7788 ; 7.281 ; 5.000 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4AYQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1290052981. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-12 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 : 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) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 154906 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 46.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.28000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PREVIOUSLY SOLVED NATIVE STRUCTURE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACTETATE, 0.1 M BIS REMARK 280 -TRIS PH 6.5, 22% WT/VOL PEG 3350 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 71.80350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 41.45577 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 16.67533 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 71.80350 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 41.45577 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 16.67533 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 71.80350 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 41.45577 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 16.67533 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 82.91154 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 33.35067 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 82.91154 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 33.35067 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 82.91154 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 33.35067 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 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 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 MET A 24 REMARK 465 ALA A 25 REMARK 465 SER A 26 REMARK 465 GLU A 27 REMARK 465 THR A 28 REMARK 465 LEU A 463 REMARK 465 GLU A 464 REMARK 465 HIS A 465 REMARK 465 HIS A 466 REMARK 465 HIS A 467 REMARK 465 HIS A 468 REMARK 465 HIS A 469 REMARK 465 HIS A 470 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 THR A 29 OG1 CG2 REMARK 470 VAL A 462 CG1 CG2 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 C4 PEG A 506 O1 PEG A 507 1.47 REMARK 500 C2 PEG A 506 O HOH A 2472 1.97 REMARK 500 C1 PEG A 504 O1 PEG A 505 2.00 REMARK 500 O HOH A 2649 O HOH A 2650 2.08 REMARK 500 O HOH A 2251 O HOH A 2252 2.17 REMARK 500 O2 PEG A 506 O HOH A 2472 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 2456 O HOH A 2746 1554 2.02 REMARK 500 O HOH A 2121 O HOH A 2845 2555 2.03 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 ARG A 125 NE - CZ - NH2 ANGL. DEV. = -4.7 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 55 29.17 -144.16 REMARK 500 ASP A 178 91.54 67.15 REMARK 500 THR A 181 -161.15 -109.72 REMARK 500 ASP A 245 -96.35 -123.58 REMARK 500 TYR A 247 -4.15 74.11 REMARK 500 ALA A 248 -36.10 -143.19 REMARK 500 ASP A 249 -74.85 -18.20 REMARK 500 GLU A 427 -86.99 -96.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A2039 DISTANCE = 7.13 ANGSTROMS REMARK 525 HOH A2041 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A2065 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH A2066 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A2072 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH A2078 DISTANCE = 7.01 ANGSTROMS REMARK 525 HOH A2079 DISTANCE = 7.15 ANGSTROMS REMARK 525 HOH A2139 DISTANCE = 6.47 ANGSTROMS REMARK 525 HOH A2141 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A2142 DISTANCE = 7.73 ANGSTROMS REMARK 525 HOH A2192 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A2217 DISTANCE = 6.80 ANGSTROMS REMARK 525 HOH A2339 DISTANCE = 6.28 ANGSTROMS REMARK 525 HOH A2346 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A2433 DISTANCE = 6.44 ANGSTROMS 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 PEG A 504 REMARK 610 PEG A 506 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 NA A 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 84 O REMARK 620 2 ASP A 87 OD1 98.9 REMARK 620 3 SER A 426 OG 89.2 100.6 REMARK 620 4 ASN A 454 OD1 160.8 99.9 91.2 REMARK 620 5 HOH A2201 O 90.3 81.4 178.0 88.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 253 OE2 REMARK 620 2 HOH A2556 O 99.2 REMARK 620 3 HOH A2557 O 96.9 79.2 REMARK 620 4 HOH A2558 O 90.1 164.3 87.2 REMARK 620 5 HOH A2559 O 89.7 85.2 163.8 107.7 REMARK 620 6 HOH A2658 O 171.7 88.4 87.8 83.2 87.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 500 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 451 O REMARK 620 2 THR A 451 OG1 72.4 REMARK 620 3 MVL A 503 O3 71.8 123.1 REMARK 620 4 MVL A 503 O2 88.3 70.7 65.5 REMARK 620 5 HOH A2554 O 142.2 70.2 135.6 84.5 REMARK 620 6 HOH A2555 O 86.3 74.8 143.1 145.0 79.0 REMARK 620 7 HOH A2722 O 145.3 132.4 73.6 80.9 69.7 120.6 REMARK 620 8 HOH A2723 O 89.7 146.4 74.6 138.6 119.5 75.9 77.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MVL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 508 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4AYO RELATED DB: PDB REMARK 900 STRUCTURE OF THE GH47 PROCESSING ALPHA-1,2-MANNOSIDASE FROM REMARK 900 CAULOBACTER STRAIN K31 REMARK 900 RELATED ID: 4AYP RELATED DB: PDB REMARK 900 STRUCTURE OF THE GH47 PROCESSING ALPHA-1,2-MANNOSIDASE FROM REMARK 900 CAULOBACTER STRAIN K31 IN COMPLEX WITH THIOMANNOBIOSIDE REMARK 900 RELATED ID: 4AYR RELATED DB: PDB REMARK 900 STRUCTURE OF THE GH47 PROCESSING ALPHA-1,2-MANNOSIDASE FROM REMARK 900 CAULOBACTER STRAIN K31 IN COMPLEX WITH NOEUROMYCIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 N-TERMINAL TRUNCATION TO REMOVE SIGNAL PEPTIDE DBREF 4AYQ A 27 462 UNP B0SWV2 B0SWV2_CAUSK 27 462 SEQADV 4AYQ MET A 24 UNP B0SWV2 EXPRESSION TAG SEQADV 4AYQ ALA A 25 UNP B0SWV2 EXPRESSION TAG SEQADV 4AYQ SER A 26 UNP B0SWV2 EXPRESSION TAG SEQADV 4AYQ LEU A 463 UNP B0SWV2 EXPRESSION TAG SEQADV 4AYQ GLU A 464 UNP B0SWV2 EXPRESSION TAG SEQADV 4AYQ HIS A 465 UNP B0SWV2 EXPRESSION TAG SEQADV 4AYQ HIS A 466 UNP B0SWV2 EXPRESSION TAG SEQADV 4AYQ HIS A 467 UNP B0SWV2 EXPRESSION TAG SEQADV 4AYQ HIS A 468 UNP B0SWV2 EXPRESSION TAG SEQADV 4AYQ HIS A 469 UNP B0SWV2 EXPRESSION TAG SEQADV 4AYQ HIS A 470 UNP B0SWV2 EXPRESSION TAG SEQRES 1 A 447 MET ALA SER GLU THR THR PRO GLU ASP TRP LYS ALA LEU SEQRES 2 A 447 ALA ALA ASP VAL ARG SER GLU PHE GLN TRP ALA TRP GLN SEQRES 3 A 447 GLY TYR VAL ALA LYS ALA TRP GLY LYS ASP GLU ILE ASN SEQRES 4 A 447 PRO VAL SER GLY THR SER ARG SER PHE PHE ILE GLU GLY SEQRES 5 A 447 HIS ASP LEU GLY LEU SER LEU VAL GLU ALA LEU ASP THR SEQRES 6 A 447 LEU TRP ILE MET GLY LEU ASP ALA GLU PHE GLN ALA GLY SEQRES 7 A 447 VAL ASP TRP VAL LYS ALA ASN LEU SER PHE ASP VAL ASP SEQRES 8 A 447 GLY ASN ALA GLN VAL PHE GLU THR ASN ILE ARG LEU VAL SEQRES 9 A 447 GLY GLY LEU LEU SER ALA HIS LEU ALA SER GLY ASP PRO SEQRES 10 A 447 VAL LEU LEU ALA LYS ALA ARG ASP LEU ALA ASP ARG LEU SEQRES 11 A 447 ALA LYS ALA PHE GLU ALA SER PRO HIS GLY LEU PRO TRP SEQRES 12 A 447 ARG TYR VAL ASN LEU ARG THR GLY ALA VAL SER ASP PRO SEQRES 13 A 447 GLU THR ASN LEU ALA GLU ILE GLY THR TYR LEU SER GLU SEQRES 14 A 447 PHE GLY VAL LEU SER GLN LEU THR GLY GLU ARG LYS TYR SEQRES 15 A 447 PHE ASP MET ALA LYS ARG ALA MET ARG HIS THR LEU ASP SEQRES 16 A 447 ARG ARG SER LYS ILE GLY LEU MET ALA ALA ASN ILE HIS SEQRES 17 A 447 ALA MET THR GLY ALA PHE THR SER ARG ASN ALA SER ILE SEQRES 18 A 447 ASP VAL TYR ALA ASP SER PHE TYR GLU TYR LEU TRP ASP SEQRES 19 A 447 ALA TRP ALA LEU PHE GLY ASP GLU ASP CYS LYS ARG TRP SEQRES 20 A 447 ALA VAL GLU CYS VAL ASP ALA GLN LEU ALA HIS GLN ALA SEQRES 21 A 447 LYS ARG TYR ASP GLY ARG LEU TRP PHE PRO MET VAL ASP SEQRES 22 A 447 PHE GLU THR GLY ALA VAL THR GLY THR ALA GLN SER GLU SEQRES 23 A 447 LEU ALA ALA TYR TYR ALA GLY LEU LEU GLY GLN VAL GLY SEQRES 24 A 447 ARG LYS ALA GLN GLY ASP ASP TYR LEU ALA SER PHE THR SEQRES 25 A 447 TYR LEU GLN ALA THR PHE GLY VAL ILE PRO GLU SER ILE SEQRES 26 A 447 ASP VAL THR THR GLY GLN PRO ARG ARG LYS HIS THR GLY SEQRES 27 A 447 LEU ARG PRO GLU TYR PRO ASP ALA CYS LEU ASN LEU TRP SEQRES 28 A 447 LEU ILE ASP ARG ASP PRO ARG TYR ARG ARG LEU ALA ALA SEQRES 29 A 447 ILE HIS TYR ARG GLU MET LYS ALA THR SER ARG ALA ALA SEQRES 30 A 447 PHE GLY TYR THR ALA LEU LYS ASP ILE THR THR ARG PRO SEQRES 31 A 447 MET THR GLN ASP ASP ASN CYS PRO GLY TYR TRP TRP SER SEQRES 32 A 447 GLU GLN MET LYS TYR TYR TYR LEU LEU PHE SER ASP THR SEQRES 33 A 447 PRO ARG ILE ASP TYR GLY GLN LEU GLN LEU SER THR GLU SEQRES 34 A 447 ALA ASN VAL LEU ARG GLY PHE ARG LYS VAL LEU GLU HIS SEQRES 35 A 447 HIS HIS HIS HIS HIS HET CA A 500 1 HET CA A 501 1 HET NA A 502 1 HET MVL A 503 14 HET PEG A 504 6 HET PEG A 505 7 HET PEG A 506 6 HET PEG A 507 7 HET PEG A 508 7 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM MVL (5R,6R,7S,8R)-5-(HYDROXYMETHYL)-5,6,7,8- HETNAM 2 MVL TETRAHYDROIMIDAZO[1,2-A]PYRIDINE-6,7,8-TRIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN MVL MANNOIMIDAZOLE FORMUL 2 CA 2(CA 2+) FORMUL 4 NA NA 1+ FORMUL 5 MVL C8 H12 N2 O4 FORMUL 6 PEG 5(C4 H10 O3) FORMUL 11 HOH *827(H2 O) HELIX 1 1 ASP A 32 TRP A 56 1 25 HELIX 2 2 GLY A 79 MET A 92 1 14 HELIX 3 3 LEU A 94 LEU A 109 1 16 HELIX 4 4 VAL A 119 GLY A 138 1 20 HELIX 5 5 ASP A 139 ALA A 159 1 21 HELIX 6 6 LEU A 183 GLY A 187 1 5 HELIX 7 7 TYR A 189 GLY A 201 1 13 HELIX 8 8 ARG A 203 ASP A 218 1 16 HELIX 9 9 ALA A 248 GLY A 263 1 16 HELIX 10 10 ASP A 264 GLN A 282 1 19 HELIX 11 11 ALA A 312 VAL A 321 1 10 HELIX 12 12 ARG A 323 GLY A 342 1 20 HELIX 13 13 PRO A 364 ARG A 378 1 15 HELIX 14 14 ASP A 379 SER A 397 1 19 HELIX 15 15 PRO A 421 GLU A 427 1 7 HELIX 16 16 GLU A 427 ASP A 438 1 12 SHEET 1 AA 2 GLU A 60 ASN A 62 0 SHEET 2 AA 2 THR A 67 ARG A 69 -1 O THR A 67 N ASN A 62 SHEET 1 AB 3 ASN A 116 GLN A 118 0 SHEET 2 AB 3 TYR A 168 ASN A 170 -1 O VAL A 169 N ALA A 117 SHEET 3 AB 3 VAL A 176 SER A 177 -1 O SER A 177 N TYR A 168 SHEET 1 AC 2 GLU A 180 ASN A 182 0 SHEET 2 AC 2 ASN A 229 HIS A 231 -1 O ILE A 230 N THR A 181 SHEET 1 AD 2 ASN A 241 ALA A 242 0 SHEET 2 AD 2 VAL A 295 ASP A 296 -1 O VAL A 295 N ALA A 242 SHEET 1 AE 2 LYS A 284 TYR A 286 0 SHEET 2 AE 2 ARG A 289 TRP A 291 -1 O ARG A 289 N TYR A 286 SHEET 1 AF 2 ALA A 306 SER A 308 0 SHEET 2 AF 2 SER A 347 ASP A 349 -1 O ILE A 348 N GLN A 307 SHEET 1 AG 2 ARG A 398 ALA A 399 0 SHEET 2 AG 2 GLY A 402 TYR A 403 -1 O GLY A 402 N ALA A 399 SHEET 1 AH 2 LEU A 406 ASP A 408 0 SHEET 2 AH 2 THR A 415 GLN A 416 -1 O THR A 415 N LYS A 407 SHEET 1 AI 2 GLN A 448 LEU A 449 0 SHEET 2 AI 2 VAL A 455 ARG A 457 -1 N LEU A 456 O GLN A 448 LINK O GLU A 84 NA NA A 502 1555 1555 2.38 LINK OD1 ASP A 87 NA NA A 502 1555 1555 2.43 LINK OE2 GLU A 253 CA CA A 501 1555 1555 2.31 LINK OG SER A 426 NA NA A 502 1555 1555 2.59 LINK O THR A 451 CA CA A 500 1555 1555 2.48 LINK OG1 THR A 451 CA CA A 500 1555 1555 2.52 LINK OD1 ASN A 454 NA NA A 502 1555 1555 2.33 LINK CA CA A 500 O3 MVL A 503 1555 1555 2.47 LINK CA CA A 500 O2 MVL A 503 1555 1555 2.46 LINK CA CA A 500 O HOH A2554 1555 1555 2.48 LINK CA CA A 500 O HOH A2555 1555 1555 2.41 LINK CA CA A 500 O HOH A2722 1555 1555 2.39 LINK CA CA A 500 O HOH A2723 1555 1555 2.41 LINK CA CA A 501 O HOH A2556 1555 1555 2.36 LINK CA CA A 501 O HOH A2557 1555 1555 2.34 LINK CA CA A 501 O HOH A2558 1555 1555 2.32 LINK CA CA A 501 O HOH A2559 1555 1555 2.32 LINK CA CA A 501 O HOH A2658 1555 1555 2.37 LINK NA NA A 502 O HOH A2201 1555 1555 2.49 CISPEP 1 ARG A 412 PRO A 413 0 -1.86 CISPEP 2 ARG A 412 PRO A 413 0 -2.15 SITE 1 AC1 6 THR A 451 MVL A 503 HOH A2554 HOH A2555 SITE 2 AC1 6 HOH A2722 HOH A2723 SITE 1 AC2 6 GLU A 253 HOH A2556 HOH A2557 HOH A2558 SITE 2 AC2 6 HOH A2559 HOH A2658 SITE 1 AC3 5 GLU A 84 ASP A 87 SER A 426 ASN A 454 SITE 2 AC3 5 HOH A2201 SITE 1 AC4 15 ARG A 125 ASP A 249 LEU A 310 ARG A 363 SITE 2 AC4 15 PRO A 364 GLU A 365 TYR A 423 GLU A 427 SITE 3 AC4 15 THR A 451 GLU A 452 CA A 500 HOH A2309 SITE 4 AC4 15 HOH A2550 HOH A2722 HOH A2723 SITE 1 AC5 6 ARG A 219 LYS A 222 ILE A 223 PEG A 505 SITE 2 AC5 6 HOH A2600 HOH A2842 SITE 1 AC6 7 ASP A 218 ARG A 219 PEG A 504 PEG A 508 SITE 2 AC6 7 HOH A2509 HOH A2841 HOH A2842 SITE 1 AC7 5 SER A 197 ARG A 203 PHE A 206 PEG A 507 SITE 2 AC7 5 HOH A2472 SITE 1 AC8 4 GLY A 201 ARG A 203 PEG A 506 HOH A2121 SITE 1 AC9 6 SER A 221 GLU A 273 PEG A 505 HOH A2506 SITE 2 AC9 6 HOH A2847 HOH A2848 CRYST1 143.607 143.607 50.026 90.00 90.00 120.00 H 3 9 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 0.006963 0.004020 0.000000 0.00000 SCALE2 0.000000 0.008041 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019990 0.00000