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 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,VAGIN,DODSON 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 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 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 MASTER 259 0 0 6 3 0 0 6 0 0 0 9 END