HEADER HYDROLASE 17-JUL-06 2HPL TITLE CRYSTAL STRUCTURE OF THE MOUSE P97/PNGASE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PNGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPTIDE N-GLYCANASE; COMPND 5 EC: 3.5.1.52; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: C-TERMINAL OF MOUSE P97/VCP; COMPND 9 CHAIN: B; COMPND 10 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 CODON PLUS RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PTYB1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CHEMICALLY SYNTHESIZED. OCCURS NATURALLY IN MUS SOURCE 14 MUSCULUS (MOUSE) KEYWDS PUB DOMAIN, WINGED HELIX, P97, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.ZHAO,X.ZHOU,L.WANG,G.LI,W.LENNARZ,H.SCHINDELIN REVDAT 6 14-FEB-24 2HPL 1 REMARK REVDAT 5 18-OCT-17 2HPL 1 REMARK REVDAT 4 13-JUL-11 2HPL 1 VERSN REVDAT 3 24-FEB-09 2HPL 1 VERSN REVDAT 2 26-JUN-07 2HPL 1 EXPDTA REVDAT 1 29-MAY-07 2HPL 0 JRNL AUTH G.ZHAO,X.ZHOU,L.WANG,G.LI,H.SCHINDELIN,W.J.LENNARZ JRNL TITL STUDIES ON PEPTIDE:N-GLYCANASE-P97 INTERACTION SUGGEST THAT JRNL TITL 2 P97 PHOSPHORYLATION MODULATES ENDOPLASMIC JRNL TITL 3 RETICULUM-ASSOCIATED DEGRADATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 8785 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17496150 JRNL DOI 10.1073/PNAS.0702966104 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 8753 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) : 0.146 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 428 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 319 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 46.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE SET COUNT : 16 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 827 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 167 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.84000 REMARK 3 B22 (A**2) : -0.90000 REMARK 3 B33 (A**2) : -1.94000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.134 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.459 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 839 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 780 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1133 ; 1.479 ; 1.997 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1816 ; 0.870 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 103 ; 5.664 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 39 ;36.053 ;24.103 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 151 ;14.384 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;16.512 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 130 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 926 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 165 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 179 ; 0.229 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 774 ; 0.200 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 411 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 464 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 113 ; 0.159 ; 0.200 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): 8 ; 0.185 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 31 ; 0.313 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.173 ; 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): 681 ; 1.232 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 214 ; 0.258 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 846 ; 1.396 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 351 ; 2.515 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 287 ; 3.494 ; 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 12 A 111 REMARK 3 RESIDUE RANGE : B 803 B 806 REMARK 3 ORIGIN FOR THE GROUP (A): 40.6055 51.9203 13.9924 REMARK 3 T TENSOR REMARK 3 T11: -0.0399 T22: -0.0407 REMARK 3 T33: -0.0506 T12: 0.0127 REMARK 3 T13: -0.0029 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 0.6876 L22: 2.0500 REMARK 3 L33: 1.4068 L12: -0.0694 REMARK 3 L13: -0.1333 L23: 0.4840 REMARK 3 S TENSOR REMARK 3 S11: 0.0055 S12: 0.0282 S13: 0.0327 REMARK 3 S21: 0.0239 S22: -0.0434 S23: -0.0044 REMARK 3 S31: 0.0245 S32: -0.0204 S33: 0.0380 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 REMARK 4 REMARK 4 2HPL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-JUL-06. REMARK 100 THE DEPOSITION ID IS D_1000038612. 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 : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.04 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8764 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 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 (%) : 87.7 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 46.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.31400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: REFMAC 5.2.0005 REMARK 200 SOFTWARE USED: REFMAC 5.2.0005 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18-22% PEG 5000 MME AND 14-18% REMARK 280 TACSIMATE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 281K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 32.80400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.80400 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.21000 REMARK 290 SMTRY3 4 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 300 REMARK: HETERODIMER OF MOUSE PNGASE PUB AND P97 REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2HPJ RELATED DB: PDB REMARK 900 PUB DOMAIN OF MOUSE PNGASE DBREF 2HPL A 12 111 UNP Q9JI78 Q9JI78_MOUSE 12 111 DBREF 2HPL B 802 806 PDB 2HPL 2HPL 802 806 SEQRES 1 A 100 SER ALA SER PRO ALA VAL ALA GLU LEU CYS GLN ASN THR SEQRES 2 A 100 PRO GLU THR PHE LEU GLU ALA SER LYS LEU LEU LEU THR SEQRES 3 A 100 TYR ALA ASP ASN ILE LEU ARG ASN PRO SER ASP GLU LYS SEQRES 4 A 100 TYR ARG SER ILE ARG ILE GLY ASN THR ALA PHE SER THR SEQRES 5 A 100 ARG LEU LEU PRO VAL ARG GLY ALA VAL GLU CYS LEU PHE SEQRES 6 A 100 GLU MET GLY PHE GLU GLU GLY GLU THR HIS LEU ILE PHE SEQRES 7 A 100 PRO LYS LYS ALA SER VAL GLU GLN LEU GLN LYS ILE ARG SEQRES 8 A 100 ASP LEU ILE ALA ILE GLU ARG SER SER SEQRES 1 B 5 ASP ASP LEU TYR GLY FORMUL 3 HOH *167(H2 O) HELIX 1 1 SER A 14 CYS A 21 1 8 HELIX 2 2 THR A 24 ASN A 45 1 22 HELIX 3 3 ASP A 48 TYR A 51 5 4 HELIX 4 4 ASN A 58 LEU A 65 1 8 HELIX 5 5 GLY A 70 GLY A 79 1 10 HELIX 6 6 SER A 94 SER A 110 1 17 SHEET 1 A 3 SER A 53 ARG A 55 0 SHEET 2 A 3 HIS A 86 ILE A 88 -1 O LEU A 87 N ILE A 54 SHEET 3 A 3 GLU A 81 GLU A 82 -1 N GLU A 81 O ILE A 88 CRYST1 65.608 52.420 35.028 90.00 115.33 90.00 C 1 2 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 0.015242 0.000000 0.007215 0.00000 SCALE2 0.000000 0.019077 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031585 0.00000