HEADER HYDROLASE 30-AUG-06 2I74 TITLE CRYSTAL STRUCTURE OF MOUSE PEPTIDE N-GLYCANASE C-TERMINAL DOMAIN IN TITLE 2 COMPLEX WITH MANNOPENTAOSE CAVEAT 2I74 MAN D 1 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PNGASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, RESIDUES 471-651; COMPND 5 SYNONYM: PEPTIDE N-GLYCANASE; COMPND 6 EC: 3.5.1.52; 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 GENE: NGLY1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3 CONDON PLUS RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21B KEYWDS BETA-SANDWICH, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHOU,G.ZHAO,L.WANG,G.LI,W.J.LENNARZ,H.SCHINDELIN REVDAT 7 30-AUG-23 2I74 1 HETSYN REVDAT 6 29-JUL-20 2I74 1 CAVEAT COMPND REMARK SEQADV REVDAT 6 2 1 HETNAM LINK SITE ATOM REVDAT 5 18-OCT-17 2I74 1 REMARK REVDAT 4 13-JUL-11 2I74 1 VERSN REVDAT 3 24-FEB-09 2I74 1 VERSN REVDAT 2 28-NOV-06 2I74 1 JRNL REVDAT 1 24-OCT-06 2I74 0 JRNL AUTH X.ZHOU,G.ZHAO,J.J.TRUGLIO,L.WANG,G.LI,W.J.LENNARZ, JRNL AUTH 2 H.SCHINDELIN JRNL TITL STRUCTURAL AND BIOCHEMICAL STUDIES OF THE C-TERMINAL DOMAIN JRNL TITL 2 OF MOUSE PEPTIDE-N-GLYCANASE IDENTIFY IT AS A JRNL TITL 3 MANNOSE-BINDING MODULE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 17214 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 17088551 JRNL DOI 10.1073/PNAS.0602954103 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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 (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 35851 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1856 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) : 2401 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE SET COUNT : 128 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2915 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 132 REMARK 3 SOLVENT ATOMS : 321 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 16.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.05000 REMARK 3 B22 (A**2) : -0.59000 REMARK 3 B33 (A**2) : -0.39000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.44000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.125 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.117 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.701 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3106 ; 0.015 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2132 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4185 ; 1.543 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5129 ; 1.668 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 358 ; 6.591 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 159 ;36.553 ;24.088 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 536 ;12.526 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;14.186 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 463 ; 0.125 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3371 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 654 ; 0.000 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 520 ; 0.215 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2277 ; 0.234 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1488 ; 0.181 ; 0.500 REMARK 3 NON-BONDED TORSION OTHERS (A): 1701 ; 0.094 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 447 ; 0.215 ; 0.500 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): 16 ; 0.401 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 53 ; 0.346 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 41 ; 0.221 ; 0.500 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): 2337 ; 1.127 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 743 ; 0.251 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2864 ; 1.294 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1557 ; 2.309 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1321 ; 3.240 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 472 A 651 REMARK 3 ORIGIN FOR THE GROUP (A): 13.3227 0.3499 38.1889 REMARK 3 T TENSOR REMARK 3 T11: -0.0540 T22: -0.0282 REMARK 3 T33: -0.0323 T12: -0.0013 REMARK 3 T13: -0.0080 T23: 0.0132 REMARK 3 L TENSOR REMARK 3 L11: 1.0751 L22: 1.6480 REMARK 3 L33: 1.4257 L12: 0.2093 REMARK 3 L13: -0.5466 L23: -0.2815 REMARK 3 S TENSOR REMARK 3 S11: -0.0429 S12: -0.0191 S13: 0.0059 REMARK 3 S21: -0.0664 S22: 0.0747 S23: 0.2070 REMARK 3 S31: 0.0871 S32: -0.0811 S33: -0.0317 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 472 B 651 REMARK 3 ORIGIN FOR THE GROUP (A): 15.8492 14.3249 7.8970 REMARK 3 T TENSOR REMARK 3 T11: -0.0544 T22: -0.0649 REMARK 3 T33: -0.0670 T12: 0.0009 REMARK 3 T13: 0.0068 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 0.9560 L22: 0.9460 REMARK 3 L33: 0.9223 L12: -0.0941 REMARK 3 L13: 0.4318 L23: -0.1952 REMARK 3 S TENSOR REMARK 3 S11: -0.0168 S12: -0.0143 S13: 0.0005 REMARK 3 S21: 0.0627 S22: 0.0226 S23: 0.0574 REMARK 3 S31: -0.0800 S32: -0.0110 S33: -0.0058 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 2I74 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000039220. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35889 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : 0.08700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.0000 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) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.44100 REMARK 200 R SYM FOR SHELL (I) : 0.44100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 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: PDB ENTRY 2G9F REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19 % PEG 4000, 11.5 % ISOPROPANOL, 0.1 REMARK 280 M TRIS-HCL, PH 7.5, 0.2 M CALCIUM ACETATE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K 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 20.82300 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 APPLY THE FOLLOWING TO CHAINS: A, C 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 APPLY THE FOLLOWING TO CHAINS: B, D 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 LEU A 471 REMARK 465 LEU A 652 REMARK 465 GLU A 653 REMARK 465 HIS A 654 REMARK 465 HIS A 655 REMARK 465 HIS A 656 REMARK 465 HIS A 657 REMARK 465 HIS A 658 REMARK 465 HIS A 659 REMARK 465 LEU B 471 REMARK 465 LEU B 652 REMARK 465 GLU B 653 REMARK 465 HIS B 654 REMARK 465 HIS B 655 REMARK 465 HIS B 656 REMARK 465 HIS B 657 REMARK 465 HIS B 658 REMARK 465 HIS B 659 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 GLU A 472 CB CG CD OE1 OE2 REMARK 470 ARG A 473 CB CG CD NE CZ NH1 NH2 REMARK 470 LYS A 474 CB CG CD CE NZ 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 OE2 GLU A 522 O1 GOL A 15 2.12 REMARK 500 OG SER B 565 OG SER B 599 2.12 REMARK 500 O HOH A 253 O HOH A 313 2.18 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 82 O HOH A 268 2646 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 ARG A 473 104.14 147.50 REMARK 500 TRP A 519 -78.09 -77.75 REMARK 500 ASP A 562 -70.62 -101.50 REMARK 500 GLU A 574 -129.63 47.93 REMARK 500 ARG A 617 -154.45 64.52 REMARK 500 TRP B 519 -78.12 -72.38 REMARK 500 ASP B 562 -68.14 -103.31 REMARK 500 GLU B 574 -130.70 49.57 REMARK 500 ARG B 617 -152.11 64.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2G9F RELATED DB: PDB REMARK 900 2G9F IS THE CRYSTAL STRUCTURE OF INTEIN-TAGGED MOUSE PNGASE C- REMARK 900 TERMINAL DOMAIN DETERMINED AT 1.90 ANGSTROM RESOLUTION REMARK 900 RELATED ID: 2G9G RELATED DB: PDB REMARK 900 2G9G IS THE CRYSTAL STRUCTURE OF HIS-TAGGED MOUSE PNGASE C-TERMINAL REMARK 900 DOMAIN DETERMINED AT 2.00 ANGSTROM RESOLUTION DBREF 2I74 A 471 651 UNP Q9JI78 NGLY1_MOUSE 471 651 DBREF 2I74 B 471 651 UNP Q9JI78 NGLY1_MOUSE 471 651 SEQADV 2I74 LEU A 652 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 GLU A 653 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 HIS A 654 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 HIS A 655 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 HIS A 656 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 HIS A 657 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 HIS A 658 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 HIS A 659 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 LEU B 652 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 GLU B 653 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 HIS B 654 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 HIS B 655 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 HIS B 656 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 HIS B 657 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 HIS B 658 UNP Q9JI78 CLONING ARTIFACT SEQADV 2I74 HIS B 659 UNP Q9JI78 CLONING ARTIFACT SEQRES 1 A 189 LEU GLU ARG LYS GLU ILE LEU PHE ILE PRO SER GLU ASN SEQRES 2 A 189 GLU LYS ILE SER LYS GLN PHE HIS LEU ARG TYR ASP ILE SEQRES 3 A 189 VAL ARG ASP ARG TYR ILE ARG VAL SER ASP ASN ASN THR SEQRES 4 A 189 ASN ILE SER GLY TRP GLU ASN GLY VAL TRP LYS MET GLU SEQRES 5 A 189 SER ILE PHE ARG LYS VAL GLU LYS ASP TRP ASN MET VAL SEQRES 6 A 189 TYR LEU ALA ARG LYS GLU GLY SER SER PHE ALA TYR ILE SEQRES 7 A 189 SER TRP LYS PHE GLU CYS GLY SER ALA GLY LEU LYS VAL SEQRES 8 A 189 ASP THR VAL SER ILE ARG THR SER SER GLN SER PHE GLU SEQRES 9 A 189 SER GLY SER VAL ARG TRP LYS LEU ARG SER GLU THR ALA SEQRES 10 A 189 GLN VAL ASN LEU LEU GLY ASP LYS ASN LEU ARG SER TYR SEQRES 11 A 189 ASN ASP PHE SER GLY ALA THR GLU VAL THR LEU GLU ALA SEQRES 12 A 189 GLU LEU SER ARG GLY ASP GLY ASP VAL ALA TRP GLN HIS SEQRES 13 A 189 THR GLN LEU PHE ARG GLN SER LEU ASN ASP SER GLY GLU SEQRES 14 A 189 ASN GLY LEU GLU ILE ILE ILE THR PHE ASN ASP LEU LEU SEQRES 15 A 189 GLU HIS HIS HIS HIS HIS HIS SEQRES 1 B 189 LEU GLU ARG LYS GLU ILE LEU PHE ILE PRO SER GLU ASN SEQRES 2 B 189 GLU LYS ILE SER LYS GLN PHE HIS LEU ARG TYR ASP ILE SEQRES 3 B 189 VAL ARG ASP ARG TYR ILE ARG VAL SER ASP ASN ASN THR SEQRES 4 B 189 ASN ILE SER GLY TRP GLU ASN GLY VAL TRP LYS MET GLU SEQRES 5 B 189 SER ILE PHE ARG LYS VAL GLU LYS ASP TRP ASN MET VAL SEQRES 6 B 189 TYR LEU ALA ARG LYS GLU GLY SER SER PHE ALA TYR ILE SEQRES 7 B 189 SER TRP LYS PHE GLU CYS GLY SER ALA GLY LEU LYS VAL SEQRES 8 B 189 ASP THR VAL SER ILE ARG THR SER SER GLN SER PHE GLU SEQRES 9 B 189 SER GLY SER VAL ARG TRP LYS LEU ARG SER GLU THR ALA SEQRES 10 B 189 GLN VAL ASN LEU LEU GLY ASP LYS ASN LEU ARG SER TYR SEQRES 11 B 189 ASN ASP PHE SER GLY ALA THR GLU VAL THR LEU GLU ALA SEQRES 12 B 189 GLU LEU SER ARG GLY ASP GLY ASP VAL ALA TRP GLN HIS SEQRES 13 B 189 THR GLN LEU PHE ARG GLN SER LEU ASN ASP SER GLY GLU SEQRES 14 B 189 ASN GLY LEU GLU ILE ILE ILE THR PHE ASN ASP LEU LEU SEQRES 15 B 189 GLU HIS HIS HIS HIS HIS HIS HET MAN C 1 12 HET MAN C 2 11 HET MAN C 3 11 HET MAN C 4 11 HET MAN D 1 12 HET MAN D 2 11 HET MAN D 3 11 HET MAN D 4 11 HET ACT A 9 4 HET ACT A 11 4 HET ACT A 14 4 HET GOL A 15 6 HET GOL A 17 6 HET ACT B 10 4 HET ACT B 12 4 HET ACT B 13 4 HET GOL B 16 6 HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MAN 8(C6 H12 O6) FORMUL 5 ACT 6(C2 H3 O2 1-) FORMUL 8 GOL 3(C3 H8 O3) FORMUL 14 HOH *321(H2 O) HELIX 1 1 SER A 481 LYS A 488 1 8 HELIX 2 2 TRP A 514 VAL A 518 5 5 HELIX 3 3 GLY A 555 ALA A 557 5 3 HELIX 4 4 ASP A 619 GLN A 625 5 7 HELIX 5 5 SER B 481 LYS B 488 1 8 HELIX 6 6 TRP B 514 VAL B 518 5 5 HELIX 7 7 GLY B 555 ALA B 557 5 3 HELIX 8 8 ASP B 619 GLN B 625 5 7 SHEET 1 A 6 THR A 509 SER A 512 0 SHEET 2 A 6 ARG A 500 ARG A 503 -1 N TYR A 501 O ILE A 511 SHEET 3 A 6 GLN A 489 ASP A 495 -1 N ASP A 495 O ARG A 500 SHEET 4 A 6 LEU A 642 ASP A 650 -1 O ILE A 646 N PHE A 490 SHEET 5 A 6 LEU A 559 ARG A 567 -1 N ASP A 562 O THR A 647 SHEET 6 A 6 ARG A 598 TYR A 600 -1 O ARG A 598 N ILE A 566 SHEET 1 B 5 MET A 521 GLU A 522 0 SHEET 2 B 5 PHE A 545 GLU A 553 -1 O TYR A 547 N GLU A 522 SHEET 3 B 5 GLU A 608 SER A 616 -1 O LEU A 611 N TRP A 550 SHEET 4 B 5 SER A 577 ARG A 583 -1 N LYS A 581 O GLU A 612 SHEET 5 B 5 GLN A 588 LEU A 591 -1 O VAL A 589 N LEU A 582 SHEET 1 C 4 ILE A 524 GLU A 529 0 SHEET 2 C 4 MET A 534 ARG A 539 -1 O TYR A 536 N LYS A 527 SHEET 3 C 4 THR A 627 SER A 633 -1 O LEU A 629 N LEU A 537 SHEET 4 C 4 SER A 570 SER A 572 -1 N GLN A 571 O GLN A 628 SHEET 1 D 8 THR B 509 SER B 512 0 SHEET 2 D 8 ARG B 500 ARG B 503 -1 N ARG B 503 O THR B 509 SHEET 3 D 8 GLN B 489 ASP B 495 -1 N ASP B 495 O ARG B 500 SHEET 4 D 8 GLY B 641 ASP B 650 -1 O ILE B 646 N PHE B 490 SHEET 5 D 8 LEU B 559 SER B 572 -1 N ASP B 562 O THR B 647 SHEET 6 D 8 THR B 627 SER B 633 -1 O GLN B 628 N GLN B 571 SHEET 7 D 8 MET B 534 ARG B 539 -1 N LEU B 537 O LEU B 629 SHEET 8 D 8 ILE B 524 GLU B 529 -1 N GLU B 529 O MET B 534 SHEET 1 E 6 THR B 509 SER B 512 0 SHEET 2 E 6 ARG B 500 ARG B 503 -1 N ARG B 503 O THR B 509 SHEET 3 E 6 GLN B 489 ASP B 495 -1 N ASP B 495 O ARG B 500 SHEET 4 E 6 GLY B 641 ASP B 650 -1 O ILE B 646 N PHE B 490 SHEET 5 E 6 LEU B 559 SER B 572 -1 N ASP B 562 O THR B 647 SHEET 6 E 6 ASP B 594 TYR B 600 -1 O LYS B 595 N THR B 568 SHEET 1 F 5 MET B 521 GLU B 522 0 SHEET 2 F 5 PHE B 545 GLU B 553 -1 O TYR B 547 N GLU B 522 SHEET 3 F 5 GLU B 608 SER B 616 -1 O LEU B 611 N TRP B 550 SHEET 4 F 5 SER B 577 ARG B 583 -1 N SER B 577 O SER B 616 SHEET 5 F 5 GLN B 588 LEU B 591 -1 O VAL B 589 N LEU B 582 LINK O6 MAN C 1 C1 MAN C 2 1555 1555 1.45 LINK O3 MAN C 2 C1 MAN C 3 1555 1555 1.43 LINK O6 MAN C 2 C1 MAN C 4 1555 1555 1.44 LINK O6 MAN D 1 C1 MAN D 2 1555 1555 1.44 LINK O3 MAN D 2 C1 MAN D 3 1555 1555 1.44 LINK O6 MAN D 2 C1 MAN D 4 1555 1555 1.42 CRYST1 45.706 41.646 94.900 90.00 94.89 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 0.021879 0.000000 0.001872 0.00000 SCALE2 0.000000 0.024012 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010576 0.00000