HEADER HYDROLASE 18-FEB-11 3QRY TITLE ANALYSIS OF A NEW FAMILY OF WIDELY DISTRIBUTED METAL-INDEPENDENT ALPHA TITLE 2 MANNOSIDASES PROVIDES UNIQUE INSIGHT INTO THE PROCESSING OF N-LINKED TITLE 3 GLYCANS, STREPTOCOCCUS PNEUMONIAE SP_2144 1-DEOXYMANNOJIRIMYCIN TITLE 4 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: B, A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 GENE: SP_2144; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 STAR KEYWDS ALPHA-ALPHA SIX FOLD, GLYCOSIDE HYDROLASE, MANNOSIDASE, 1- KEYWDS 2 DEOXYMANNOJIRIMYCIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.J.GREGG,W.F.ZANDBERG,J.-H.HEHEMANN,G.E.WHITWORTH,L.E.DENG, AUTHOR 2 D.J.VOCADLO,A.B.BORASTON REVDAT 4 21-FEB-24 3QRY 1 REMARK REVDAT 3 11-MAY-11 3QRY 1 JRNL REVDAT 2 23-MAR-11 3QRY 1 JRNL REVDAT 1 09-MAR-11 3QRY 0 JRNL AUTH K.J.GREGG,W.F.ZANDBERG,J.H.HEHEMANN,G.E.WHITWORTH,L.DENG, JRNL AUTH 2 D.J.VOCADLO,A.B.BORASTON JRNL TITL ANALYSIS OF A NEW FAMILY OF WIDELY DISTRIBUTED JRNL TITL 2 METAL-INDEPENDENT {ALPHA}-MANNOSIDASES PROVIDES UNIQUE JRNL TITL 3 INSIGHT INTO THE PROCESSING OF N-LINKED GLYCANS. JRNL REF J.BIOL.CHEM. V. 286 15586 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21388958 JRNL DOI 10.1074/JBC.M111.223172 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 88818 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) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4679 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5261 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 303 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6922 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 1388 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.74000 REMARK 3 B22 (A**2) : -0.99000 REMARK 3 B33 (A**2) : -0.38000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.63000 REMARK 3 B23 (A**2) : 0.00000 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): 0.120 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.226 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7164 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9746 ; 1.401 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 860 ; 5.868 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 365 ;36.382 ;24.301 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1161 ;12.927 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;16.816 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1055 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5528 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; 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): 4259 ; 0.748 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6890 ; 1.280 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2905 ; 2.232 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2851 ; 3.571 ; 4.500 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 : 1.40 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 REMARK 4 REMARK 4 3QRY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1000064027. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 117 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 88818 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 158.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 2.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 1.2 M LISO4, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 79.40000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 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 350 REMARK 350 BIOMOLECULE: 2 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 1111 O HOH A 1362 1.82 REMARK 500 O HOH B 978 O HOH B 1074 1.93 REMARK 500 CZ3 TRP B 60 O HOH B 1322 1.95 REMARK 500 O HOH A 526 O HOH A 1199 1.95 REMARK 500 O HOH B 664 O HOH B 777 1.97 REMARK 500 NH1 ARG A 426 O HOH A 1214 2.01 REMARK 500 O HOH B 542 O HOH A 1309 2.02 REMARK 500 O HOH A 638 O HOH A 689 2.04 REMARK 500 O HOH B 1232 O HOH B 1249 2.07 REMARK 500 NH1 ARG B 18 O HOH B 809 2.08 REMARK 500 O HOH B 749 O HOH B 930 2.09 REMARK 500 O HOH B 443 O HOH B 1106 2.10 REMARK 500 O HOH B 465 O HOH B 1076 2.11 REMARK 500 O HOH A 436 O HOH A 1126 2.12 REMARK 500 OE2 GLU A 417 O HOH A 758 2.13 REMARK 500 CD GLU A 417 O HOH A 1209 2.14 REMARK 500 O HOH B 466 O HOH B 822 2.16 REMARK 500 O HOH A 478 O HOH A 1078 2.16 REMARK 500 O HOH A 488 O HOH A 1363 2.17 REMARK 500 OE1 GLU A 417 O HOH A 1209 2.17 REMARK 500 OD2 ASP A 251 O HOH A 1102 2.17 REMARK 500 OD2 ASP A 198 O HOH A 1040 2.18 REMARK 500 CG2 THR A 49 O HOH A 814 2.18 REMARK 500 O HOH B 572 O HOH B 1263 2.19 REMARK 500 O HOH B 1130 O HOH B 1153 2.19 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 ASP B 99 105.55 -170.19 REMARK 500 MET B 298 -179.33 -174.34 REMARK 500 LEU B 330 50.68 -96.07 REMARK 500 ASP B 399 89.26 -169.52 REMARK 500 ARG B 405 93.77 65.91 REMARK 500 ASP A 99 105.42 -168.38 REMARK 500 ARG A 129 50.50 -112.00 REMARK 500 ASP A 157 -169.52 -101.57 REMARK 500 LEU A 330 50.87 -95.33 REMARK 500 ARG A 354 -8.33 79.92 REMARK 500 ASP A 399 93.07 -170.05 REMARK 500 ARG A 405 99.44 64.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMJ B 427 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 428 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 429 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 430 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 427 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 428 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 429 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DMJ A 430 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QPF RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH 1-DEOXYMANNOJIRIMYCIN REMARK 900 RELATED ID: 3QSP RELATED DB: PDB DBREF 3QRY B 1 426 UNP Q97NA8 Q97NA8_STRPN 1 426 DBREF 3QRY A 1 426 UNP Q97NA8 Q97NA8_STRPN 1 426 SEQRES 1 B 426 MET VAL TYR SER LYS GLU ILE VAL ARG GLU TRP LEU ASP SEQRES 2 B 426 GLU VAL ALA GLU ARG ALA LYS ASP TYR PRO GLU TRP VAL SEQRES 3 B 426 ASP VAL PHE GLU ARG CYS TYR THR ASP THR LEU ASP ASN SEQRES 4 B 426 THR VAL GLU ILE LEU GLU ASP GLY SER THR PHE VAL LEU SEQRES 5 B 426 THR GLY ASP ILE PRO ALA MET TRP LEU ARG ASP SER THR SEQRES 6 B 426 ALA GLN LEU ARG PRO TYR LEU HIS VAL ALA LYS ARG ASP SEQRES 7 B 426 ALA LEU LEU ARG GLN THR ILE ALA GLY LEU VAL LYS ARG SEQRES 8 B 426 GLN MET THR LEU VAL LEU LYS ASP PRO TYR ALA ASN SER SEQRES 9 B 426 PHE ASN ILE GLU GLU ASN TRP LYS GLY HIS HIS GLU THR SEQRES 10 B 426 ASP HIS THR ASP LEU ASN GLY TRP ILE TRP GLU ARG LYS SEQRES 11 B 426 TYR GLU VAL ASP SER LEU CYS TYR PRO LEU GLN LEU ALA SEQRES 12 B 426 TYR LEU LEU TRP LYS GLU THR GLY GLU THR SER GLN PHE SEQRES 13 B 426 ASP GLU ILE PHE VAL ALA ALA THR LYS GLU ILE LEU HIS SEQRES 14 B 426 LEU TRP THR VAL GLU GLN ASP HIS LYS ASN SER PRO TYR SEQRES 15 B 426 ARG PHE VAL ARG ASP THR ASP ARG LYS GLU ASP THR LEU SEQRES 16 B 426 VAL ASN ASP GLY PHE GLY PRO ASP PHE ALA VAL THR GLY SEQRES 17 B 426 MET THR TRP SER ALA PHE ARG PRO SER ASP ASP CYS CYS SEQRES 18 B 426 GLN TYR SER TYR LEU ILE PRO SER ASN MET PHE ALA VAL SEQRES 19 B 426 VAL VAL LEU GLY TYR VAL GLN GLU ILE PHE ALA ALA LEU SEQRES 20 B 426 ASN LEU ALA ASP SER GLN SER VAL ILE ALA ASP ALA LYS SEQRES 21 B 426 ARG LEU GLN ASP GLU ILE GLN GLU GLY ILE LYS ASN TYR SEQRES 22 B 426 ALA TYR THR THR ASN SER LYS GLY GLU LYS ILE TYR ALA SEQRES 23 B 426 PHE GLU VAL ASP GLY LEU GLY ASN ALA SER ILE MET ASP SEQRES 24 B 426 ASP PRO ASN VAL PRO SER LEU LEU ALA ALA PRO TYR LEU SEQRES 25 B 426 GLY TYR CYS SER VAL ASP ASP GLU VAL TYR GLN ALA THR SEQRES 26 B 426 ARG ARG THR ILE LEU SER SER GLU ASN PRO TYR PHE TYR SEQRES 27 B 426 GLN GLY GLU TYR ALA SER GLY LEU GLY SER SER HIS THR SEQRES 28 B 426 PHE TYR ARG TYR ILE TRP PRO ILE ALA LEU SER ILE GLN SEQRES 29 B 426 GLY LEU THR THR ARG ASP LYS ALA GLU LYS LYS PHE LEU SEQRES 30 B 426 LEU ASP GLN LEU VAL ALA CYS ASP GLY GLY THR GLY VAL SEQRES 31 B 426 MET HIS GLU SER PHE HIS VAL ASP ASP PRO THR LEU TYR SEQRES 32 B 426 SER ARG GLU TRP PHE SER TRP ALA ASN MET MET PHE CYS SEQRES 33 B 426 GLU LEU VAL LEU ASP TYR LEU ASP ILE ARG SEQRES 1 A 426 MET VAL TYR SER LYS GLU ILE VAL ARG GLU TRP LEU ASP SEQRES 2 A 426 GLU VAL ALA GLU ARG ALA LYS ASP TYR PRO GLU TRP VAL SEQRES 3 A 426 ASP VAL PHE GLU ARG CYS TYR THR ASP THR LEU ASP ASN SEQRES 4 A 426 THR VAL GLU ILE LEU GLU ASP GLY SER THR PHE VAL LEU SEQRES 5 A 426 THR GLY ASP ILE PRO ALA MET TRP LEU ARG ASP SER THR SEQRES 6 A 426 ALA GLN LEU ARG PRO TYR LEU HIS VAL ALA LYS ARG ASP SEQRES 7 A 426 ALA LEU LEU ARG GLN THR ILE ALA GLY LEU VAL LYS ARG SEQRES 8 A 426 GLN MET THR LEU VAL LEU LYS ASP PRO TYR ALA ASN SER SEQRES 9 A 426 PHE ASN ILE GLU GLU ASN TRP LYS GLY HIS HIS GLU THR SEQRES 10 A 426 ASP HIS THR ASP LEU ASN GLY TRP ILE TRP GLU ARG LYS SEQRES 11 A 426 TYR GLU VAL ASP SER LEU CYS TYR PRO LEU GLN LEU ALA SEQRES 12 A 426 TYR LEU LEU TRP LYS GLU THR GLY GLU THR SER GLN PHE SEQRES 13 A 426 ASP GLU ILE PHE VAL ALA ALA THR LYS GLU ILE LEU HIS SEQRES 14 A 426 LEU TRP THR VAL GLU GLN ASP HIS LYS ASN SER PRO TYR SEQRES 15 A 426 ARG PHE VAL ARG ASP THR ASP ARG LYS GLU ASP THR LEU SEQRES 16 A 426 VAL ASN ASP GLY PHE GLY PRO ASP PHE ALA VAL THR GLY SEQRES 17 A 426 MET THR TRP SER ALA PHE ARG PRO SER ASP ASP CYS CYS SEQRES 18 A 426 GLN TYR SER TYR LEU ILE PRO SER ASN MET PHE ALA VAL SEQRES 19 A 426 VAL VAL LEU GLY TYR VAL GLN GLU ILE PHE ALA ALA LEU SEQRES 20 A 426 ASN LEU ALA ASP SER GLN SER VAL ILE ALA ASP ALA LYS SEQRES 21 A 426 ARG LEU GLN ASP GLU ILE GLN GLU GLY ILE LYS ASN TYR SEQRES 22 A 426 ALA TYR THR THR ASN SER LYS GLY GLU LYS ILE TYR ALA SEQRES 23 A 426 PHE GLU VAL ASP GLY LEU GLY ASN ALA SER ILE MET ASP SEQRES 24 A 426 ASP PRO ASN VAL PRO SER LEU LEU ALA ALA PRO TYR LEU SEQRES 25 A 426 GLY TYR CYS SER VAL ASP ASP GLU VAL TYR GLN ALA THR SEQRES 26 A 426 ARG ARG THR ILE LEU SER SER GLU ASN PRO TYR PHE TYR SEQRES 27 A 426 GLN GLY GLU TYR ALA SER GLY LEU GLY SER SER HIS THR SEQRES 28 A 426 PHE TYR ARG TYR ILE TRP PRO ILE ALA LEU SER ILE GLN SEQRES 29 A 426 GLY LEU THR THR ARG ASP LYS ALA GLU LYS LYS PHE LEU SEQRES 30 A 426 LEU ASP GLN LEU VAL ALA CYS ASP GLY GLY THR GLY VAL SEQRES 31 A 426 MET HIS GLU SER PHE HIS VAL ASP ASP PRO THR LEU TYR SEQRES 32 A 426 SER ARG GLU TRP PHE SER TRP ALA ASN MET MET PHE CYS SEQRES 33 A 426 GLU LEU VAL LEU ASP TYR LEU ASP ILE ARG HET DMJ B 427 11 HET EDO B 428 4 HET EDO B 429 4 HET EDO B 430 4 HET EDO A 427 4 HET EDO A 428 4 HET EDO A 429 4 HET DMJ A 430 11 HETNAM DMJ 1-DEOXYMANNOJIRIMYCIN HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 DMJ 2(C6 H13 N O4) FORMUL 4 EDO 6(C2 H6 O2) FORMUL 11 HOH *1388(H2 O) HELIX 1 1 SER B 4 ALA B 19 1 16 HELIX 2 2 TYR B 22 THR B 40 1 19 HELIX 3 3 LEU B 61 ARG B 69 1 9 HELIX 4 4 TYR B 71 LYS B 76 1 6 HELIX 5 5 ASP B 78 ASP B 99 1 22 HELIX 6 6 GLU B 132 GLY B 151 1 20 HELIX 7 7 ASP B 157 GLU B 174 1 18 HELIX 8 8 GLN B 175 SER B 180 5 6 HELIX 9 9 ARG B 190 THR B 194 5 5 HELIX 10 10 LEU B 195 PHE B 200 1 6 HELIX 11 11 ILE B 227 ASN B 248 1 22 HELIX 12 12 ASP B 251 ALA B 274 1 24 HELIX 13 13 ASP B 319 LEU B 330 1 12 HELIX 14 14 TRP B 357 THR B 367 1 11 HELIX 15 15 ASP B 370 CYS B 384 1 15 HELIX 16 16 PHE B 408 LEU B 423 1 16 HELIX 17 17 SER A 4 ALA A 19 1 16 HELIX 18 18 TYR A 22 THR A 40 1 19 HELIX 19 19 LEU A 61 ARG A 69 1 9 HELIX 20 20 PRO A 70 ARG A 77 5 8 HELIX 21 21 ASP A 78 ASP A 99 1 22 HELIX 22 22 GLU A 132 GLY A 151 1 20 HELIX 23 23 ASP A 157 GLU A 174 1 18 HELIX 24 24 GLN A 175 SER A 180 5 6 HELIX 25 25 ARG A 190 THR A 194 5 5 HELIX 26 26 LEU A 195 PHE A 200 1 6 HELIX 27 27 ILE A 227 ASN A 248 1 22 HELIX 28 28 ASP A 251 ALA A 274 1 24 HELIX 29 29 ASP A 319 LEU A 330 1 12 HELIX 30 30 TRP A 357 THR A 367 1 11 HELIX 31 31 ASP A 370 CYS A 384 1 15 HELIX 32 32 PHE A 408 LEU A 423 1 16 SHEET 1 A 2 VAL B 41 ILE B 43 0 SHEET 2 A 2 THR B 49 VAL B 51 -1 O PHE B 50 N GLU B 42 SHEET 1 B 3 ALA B 58 TRP B 60 0 SHEET 2 B 3 SER B 104 ASN B 106 -1 O PHE B 105 N MET B 59 SHEET 3 B 3 ILE B 126 GLU B 128 -1 O TRP B 127 N SER B 104 SHEET 1 C 2 ASP B 118 HIS B 119 0 SHEET 2 C 2 VAL B 185 ARG B 186 -1 O VAL B 185 N HIS B 119 SHEET 1 D 2 TYR B 225 LEU B 226 0 SHEET 2 D 2 GLU B 288 VAL B 289 -1 O VAL B 289 N TYR B 225 SHEET 1 E 2 TYR B 275 THR B 277 0 SHEET 2 E 2 LYS B 283 TYR B 285 -1 O ILE B 284 N THR B 276 SHEET 1 F 2 PHE B 337 GLN B 339 0 SHEET 2 F 2 SER B 344 LEU B 346 -1 O GLY B 345 N TYR B 338 SHEET 1 G 3 TYR B 355 ILE B 356 0 SHEET 2 G 3 SER B 394 HIS B 396 -1 O PHE B 395 N ILE B 356 SHEET 3 G 3 ASP B 399 SER B 404 -1 O LEU B 402 N HIS B 396 SHEET 1 H 2 VAL A 41 ILE A 43 0 SHEET 2 H 2 THR A 49 VAL A 51 -1 O PHE A 50 N GLU A 42 SHEET 1 I 3 MET A 59 TRP A 60 0 SHEET 2 I 3 SER A 104 PHE A 105 -1 O PHE A 105 N MET A 59 SHEET 3 I 3 ILE A 126 GLU A 128 -1 O TRP A 127 N SER A 104 SHEET 1 J 2 ASP A 118 HIS A 119 0 SHEET 2 J 2 VAL A 185 ARG A 186 -1 O VAL A 185 N HIS A 119 SHEET 1 K 2 TYR A 225 LEU A 226 0 SHEET 2 K 2 GLU A 288 VAL A 289 -1 O VAL A 289 N TYR A 225 SHEET 1 L 2 TYR A 275 THR A 277 0 SHEET 2 L 2 LYS A 283 TYR A 285 -1 O ILE A 284 N THR A 276 SHEET 1 M 2 PHE A 337 GLN A 339 0 SHEET 2 M 2 SER A 344 LEU A 346 -1 O GLY A 345 N TYR A 338 SHEET 1 N 3 TYR A 355 ILE A 356 0 SHEET 2 N 3 SER A 394 HIS A 396 -1 O PHE A 395 N ILE A 356 SHEET 3 N 3 ASP A 399 SER A 404 -1 O LEU A 402 N HIS A 396 CISPEP 1 VAL B 303 PRO B 304 0 2.80 CISPEP 2 VAL A 303 PRO A 304 0 9.76 SITE 1 AC1 14 THR B 53 TRP B 60 ARG B 62 ASP B 63 SITE 2 AC1 14 PRO B 216 SER B 217 ASP B 218 ASN B 302 SITE 3 AC1 14 HIS B 350 TRP B 357 ARG B 405 TRP B 410 SITE 4 AC1 14 HOH B 629 HOH B 780 SITE 1 AC2 4 ASP B 251 SER B 252 GLN B 253 HOH B 968 SITE 1 AC3 6 ARG B 69 GLU B 149 GLU B 417 HOH B 599 SITE 2 AC3 6 HOH B 932 HOH B1100 SITE 1 AC4 5 GLU B 14 ILE B 425 HOH B 970 HOH B1027 SITE 2 AC4 5 HOH B1049 SITE 1 AC5 3 ASN A 197 ASP A 198 HOH A 438 SITE 1 AC6 2 SER A 316 ARG A 369 SITE 1 AC7 2 GLU A 14 HOH A1227 SITE 1 AC8 14 TRP A 60 ARG A 62 ASP A 63 PRO A 216 SITE 2 AC8 14 ASP A 218 ASN A 302 HIS A 350 TRP A 357 SITE 3 AC8 14 ARG A 405 PHE A 408 TRP A 410 HOH A 478 SITE 4 AC8 14 HOH A 533 HOH A1078 CRYST1 53.460 158.800 60.040 90.00 107.19 90.00 P 1 21 1 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 0.018706 0.000000 0.005787 0.00000 SCALE2 0.000000 0.006297 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017434 0.00000