HEADER PROTEIN TRANSPORT 10-MAR-05 1Z2W TITLE CRYSTAL STRUCTURE OF MOUSE VPS29 COMPLEXED WITH MN2+ CAVEAT 1Z2W CHIRALITY ERROR AT THE CA CENTER OF CYS A 41 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING 29; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: VESICLE PROTEIN SORTING 29, VPS29; COMPND 5 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: VPS29; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)/PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T-2 KEYWDS VPS29, RETROMER, PHOSPHATASE, MANGANESE, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR B.M.COLLINS,C.F.SKINNER,P.J.WATSON,M.N.J.SEAMAN,D.J.OWEN REVDAT 5 25-OCT-23 1Z2W 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 1Z2W 1 VERSN REVDAT 3 24-FEB-09 1Z2W 1 VERSN REVDAT 2 02-AUG-05 1Z2W 1 JRNL REVDAT 1 21-JUN-05 1Z2W 0 JRNL AUTH B.M.COLLINS,C.F.SKINNER,P.J.WATSON,M.N.J.SEAMAN,D.J.OWEN JRNL TITL VPS29 HAS A PHOSPHOESTERASE FOLD THAT ACTS AS A PROTEIN JRNL TITL 2 INTERACTION SCAFFOLD FOR RETROMER ASSEMBLY JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 594 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 15965486 JRNL DOI 10.1038/NSMB954 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 27724 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) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1486 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1865 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.3080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2892 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 316 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.86 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.34000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : -0.48000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.93000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.169 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.166 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.116 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.160 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2983 ; 0.026 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2717 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4035 ; 2.134 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6349 ; 1.073 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 362 ; 7.664 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 458 ; 0.238 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3252 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 570 ; 0.009 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 584 ; 0.223 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3049 ; 0.261 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1775 ; 0.095 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 245 ; 0.284 ; 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): 14 ; 0.306 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 48 ; 0.322 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 27 ; 0.147 ; 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): 1808 ; 1.432 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2934 ; 2.580 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1175 ; 3.459 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1101 ; 5.427 ; 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 : BABINET MODEL WITH 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 1Z2W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAR-05. REMARK 100 THE DEPOSITION ID IS D_1000032229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 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 : NULL REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30024 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 57.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.700 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.44100 REMARK 200 R SYM FOR SHELL (I) : 0.52500 REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 1Z2X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 0.2M NACL, 20% PEG3000, PH REMARK 280 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 34.47650 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, 3 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: BIOLOGICAL UNIT IS BELEIVED TO BE MONOMER 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 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 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL 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 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 GLY A -9 REMARK 465 SER A -8 REMARK 465 PRO A -7 REMARK 465 GLU A -6 REMARK 465 PHE A -5 REMARK 465 GLY A -4 REMARK 465 THR A -3 REMARK 465 ARG A -2 REMARK 465 ASP A -1 REMARK 465 ARG A 0 REMARK 465 GLY B -9 REMARK 465 SER B -8 REMARK 465 PRO B -7 REMARK 465 GLU B -6 REMARK 465 PHE B -5 REMARK 465 GLY B -4 REMARK 465 THR B -3 REMARK 465 ARG B -2 REMARK 465 ASP B -1 REMARK 465 ARG B 0 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 B 771 O HOH B 834 1.36 REMARK 500 O HOH B 781 O HOH B 823 1.91 REMARK 500 O HOH A 613 O HOH A 736 1.93 REMARK 500 OD2 ASP B 171 O HOH B 772 1.98 REMARK 500 O HOH B 764 O HOH B 783 2.00 REMARK 500 NZ LYS A 21 O ASP A 170 2.02 REMARK 500 O ASN A 145 O HOH A 733 2.09 REMARK 500 O HOH A 655 O HOH A 656 2.10 REMARK 500 O HOH A 737 O HOH A 777 2.11 REMARK 500 O HOH B 737 O HOH B 804 2.14 REMARK 500 SG CYS B 15 O HOH B 764 2.15 REMARK 500 OH TYR B 163 O HOH B 795 2.15 REMARK 500 O GLN A 89 O HOH A 613 2.16 REMARK 500 O HOH A 638 O HOH A 741 2.17 REMARK 500 CB TRP A 93 O HOH B 839 2.17 REMARK 500 O HOH B 805 O HOH B 807 2.18 REMARK 500 O HOH A 656 O HOH A 712 2.18 REMARK 500 O2 GOL A 505 O HOH A 698 2.18 REMARK 500 O HOH B 763 O HOH B 791 2.19 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 CYS A 41 N - CA - CB ANGL. DEV. = 9.2 DEGREES REMARK 500 ASP A 64 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 104 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 VAL A 108 CG1 - CB - CG2 ANGL. DEV. = 13.5 DEGREES REMARK 500 ASP A 171 CB - CG - OD2 ANGL. DEV. = 8.2 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ASP B 8 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 LEU B 40 O - C - N ANGL. DEV. = 11.0 DEGREES REMARK 500 CYS B 41 C - N - CA ANGL. DEV. = 22.5 DEGREES REMARK 500 CYS B 41 CB - CA - C ANGL. DEV. = 7.6 DEGREES REMARK 500 CYS B 41 CA - CB - SG ANGL. DEV. = -12.4 DEGREES REMARK 500 ASP B 62 CB - CG - OD2 ANGL. DEV. = 10.1 DEGREES REMARK 500 ARG B 104 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP B 171 CB - CG - OD1 ANGL. DEV. = 5.7 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 CYS A 41 -140.03 82.15 REMARK 500 HIS A 115 -53.75 80.38 REMARK 500 ALA A 121 109.37 -160.03 REMARK 500 ASN A 140 -163.52 -114.45 REMARK 500 ASN A 145 53.64 -107.06 REMARK 500 ALA A 157 -118.04 58.89 REMARK 500 CYS B 41 -30.37 104.77 REMARK 500 ASP B 107 52.91 -95.42 REMARK 500 HIS B 115 -41.03 66.96 REMARK 500 ALA B 157 -124.02 63.51 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 40 CYS A 41 -149.26 REMARK 500 PRO B 92 TRP B 93 -143.10 REMARK 500 REMARK 500 REMARK: NULL 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 MN A 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD1 REMARK 620 2 HIS A 10 NE2 123.7 REMARK 620 3 ASN A 39 OD1 86.7 91.1 REMARK 620 4 HIS A 117 NE2 91.6 95.2 173.4 REMARK 620 5 HOH A 603 O 100.0 134.6 78.8 95.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 602 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 39 OD1 REMARK 620 2 ASP A 62 OD1 93.7 REMARK 620 3 HIS A 86 NE2 85.2 90.4 REMARK 620 4 HIS A 115 ND1 161.8 102.9 87.1 REMARK 620 5 HOH A 603 O 79.4 153.4 114.3 88.8 REMARK 620 6 HOH A 693 O 81.7 70.1 155.6 110.9 83.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 701 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 8 OD1 REMARK 620 2 HIS B 10 NE2 121.7 REMARK 620 3 ASN B 39 OD1 85.4 86.9 REMARK 620 4 HIS B 117 NE2 91.9 95.4 177.1 REMARK 620 5 HOH B 703 O 105.1 129.0 77.2 102.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 702 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 39 OD1 REMARK 620 2 ASP B 62 OD2 95.3 REMARK 620 3 HIS B 86 NE2 79.5 89.9 REMARK 620 4 HIS B 115 ND1 159.2 105.4 98.3 REMARK 620 5 HOH B 703 O 77.5 151.5 115.2 85.0 REMARK 620 6 HOH B 770 O 85.0 77.2 158.9 101.2 74.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 505 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1S3M RELATED DB: PDB REMARK 900 ARCHAEAL MJ0936, A VPS29 RELATED PHOSPHOESTERASE REMARK 900 RELATED ID: 1S3N RELATED DB: PDB REMARK 900 ARCHAEAL MJ0936, A VPS29 RELATED PHOSPHOESTERASE REMARK 900 RELATED ID: 1Z2X RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH NO BOUND MANGANESE DBREF 1Z2W A 1 182 UNP Q9QZ88 VPS29_MOUSE 1 182 DBREF 1Z2W B 1 182 UNP Q9QZ88 VPS29_MOUSE 1 182 SEQADV 1Z2W GLY A -9 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W SER A -8 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W PRO A -7 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W GLU A -6 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W PHE A -5 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W GLY A -4 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W THR A -3 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W ARG A -2 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W ASP A -1 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W ARG A 0 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W GLY B -9 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W SER B -8 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W PRO B -7 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W GLU B -6 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W PHE B -5 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W GLY B -4 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W THR B -3 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W ARG B -2 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W ASP B -1 UNP Q9QZ88 CLONING ARTIFACT SEQADV 1Z2W ARG B 0 UNP Q9QZ88 CLONING ARTIFACT SEQRES 1 A 192 GLY SER PRO GLU PHE GLY THR ARG ASP ARG MET LEU VAL SEQRES 2 A 192 LEU VAL LEU GLY ASP LEU HIS ILE PRO HIS ARG CYS ASN SEQRES 3 A 192 SER LEU PRO ALA LYS PHE LYS LYS LEU LEU VAL PRO GLY SEQRES 4 A 192 LYS ILE GLN HIS ILE LEU CYS THR GLY ASN LEU CYS THR SEQRES 5 A 192 LYS GLU SER TYR ASP TYR LEU LYS THR LEU ALA GLY ASP SEQRES 6 A 192 VAL HIS ILE VAL ARG GLY ASP PHE ASP GLU ASN LEU ASN SEQRES 7 A 192 TYR PRO GLU GLN LYS VAL VAL THR VAL GLY GLN PHE LYS SEQRES 8 A 192 ILE GLY LEU ILE HIS GLY HIS GLN VAL ILE PRO TRP GLY SEQRES 9 A 192 ASP MET ALA SER LEU ALA LEU LEU GLN ARG GLN PHE ASP SEQRES 10 A 192 VAL ASP ILE LEU ILE SER GLY HIS THR HIS LYS PHE GLU SEQRES 11 A 192 ALA PHE GLU HIS GLU ASN LYS PHE TYR ILE ASN PRO GLY SEQRES 12 A 192 SER ALA THR GLY ALA TYR ASN ALA LEU GLU THR ASN ILE SEQRES 13 A 192 ILE PRO SER PHE VAL LEU MET ASP ILE GLN ALA SER THR SEQRES 14 A 192 VAL VAL THR TYR VAL TYR GLN LEU ILE GLY ASP ASP VAL SEQRES 15 A 192 LYS VAL GLU ARG ILE GLU TYR LYS LYS SER SEQRES 1 B 192 GLY SER PRO GLU PHE GLY THR ARG ASP ARG MET LEU VAL SEQRES 2 B 192 LEU VAL LEU GLY ASP LEU HIS ILE PRO HIS ARG CYS ASN SEQRES 3 B 192 SER LEU PRO ALA LYS PHE LYS LYS LEU LEU VAL PRO GLY SEQRES 4 B 192 LYS ILE GLN HIS ILE LEU CYS THR GLY ASN LEU CYS THR SEQRES 5 B 192 LYS GLU SER TYR ASP TYR LEU LYS THR LEU ALA GLY ASP SEQRES 6 B 192 VAL HIS ILE VAL ARG GLY ASP PHE ASP GLU ASN LEU ASN SEQRES 7 B 192 TYR PRO GLU GLN LYS VAL VAL THR VAL GLY GLN PHE LYS SEQRES 8 B 192 ILE GLY LEU ILE HIS GLY HIS GLN VAL ILE PRO TRP GLY SEQRES 9 B 192 ASP MET ALA SER LEU ALA LEU LEU GLN ARG GLN PHE ASP SEQRES 10 B 192 VAL ASP ILE LEU ILE SER GLY HIS THR HIS LYS PHE GLU SEQRES 11 B 192 ALA PHE GLU HIS GLU ASN LYS PHE TYR ILE ASN PRO GLY SEQRES 12 B 192 SER ALA THR GLY ALA TYR ASN ALA LEU GLU THR ASN ILE SEQRES 13 B 192 ILE PRO SER PHE VAL LEU MET ASP ILE GLN ALA SER THR SEQRES 14 B 192 VAL VAL THR TYR VAL TYR GLN LEU ILE GLY ASP ASP VAL SEQRES 15 B 192 LYS VAL GLU ARG ILE GLU TYR LYS LYS SER HET MN A 601 1 HET MN A 602 1 HET GOL A 501 6 HET GOL A 502 6 HET GOL A 505 6 HET MN B 701 1 HET MN B 702 1 HET GOL B 503 6 HET GOL B 504 6 HETNAM MN MANGANESE (II) ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MN 4(MN 2+) FORMUL 5 GOL 5(C3 H8 O3) FORMUL 12 HOH *316(H2 O) HELIX 1 1 PRO A 19 LYS A 24 1 6 HELIX 2 2 THR A 42 ALA A 53 1 12 HELIX 3 3 ASP A 95 ASP A 107 1 13 HELIX 4 4 PRO B 19 LYS B 24 1 6 HELIX 5 5 THR B 42 ALA B 53 1 12 HELIX 6 6 ASP B 95 ASP B 107 1 13 SHEET 1 A 6 ASP A 55 ILE A 58 0 SHEET 2 A 6 HIS A 33 CYS A 36 1 N CYS A 36 O HIS A 57 SHEET 3 A 6 LEU A 2 LEU A 6 1 N LEU A 4 O LEU A 35 SHEET 4 A 6 SER A 149 GLN A 156 -1 O VAL A 151 N VAL A 5 SHEET 5 A 6 THR A 159 ILE A 168 -1 O TYR A 163 N LEU A 152 SHEET 6 A 6 ASP A 171 LYS A 180 -1 O ILE A 177 N THR A 162 SHEET 1 B 5 GLN A 72 VAL A 77 0 SHEET 2 B 5 PHE A 80 ILE A 85 -1 O ILE A 82 N VAL A 75 SHEET 3 B 5 ILE A 110 ILE A 112 1 O ILE A 110 N GLY A 83 SHEET 4 B 5 LYS A 127 ASN A 131 1 O ILE A 130 N LEU A 111 SHEET 5 B 5 GLU A 120 HIS A 124 -1 N PHE A 122 O TYR A 129 SHEET 1 C 6 ASP B 55 ILE B 58 0 SHEET 2 C 6 HIS B 33 CYS B 36 1 N CYS B 36 O HIS B 57 SHEET 3 C 6 LEU B 2 LEU B 6 1 N LEU B 4 O LEU B 35 SHEET 4 C 6 SER B 149 GLN B 156 -1 O MET B 153 N VAL B 3 SHEET 5 C 6 THR B 159 ILE B 168 -1 O TYR B 163 N LEU B 152 SHEET 6 C 6 ASP B 171 LYS B 180 -1 O ILE B 177 N THR B 162 SHEET 1 D 5 GLN B 72 VAL B 77 0 SHEET 2 D 5 PHE B 80 ILE B 85 -1 O ILE B 82 N VAL B 75 SHEET 3 D 5 ILE B 110 SER B 113 1 O ILE B 110 N GLY B 83 SHEET 4 D 5 LYS B 127 ASN B 131 1 O PHE B 128 N LEU B 111 SHEET 5 D 5 GLU B 120 HIS B 124 -1 N PHE B 122 O TYR B 129 LINK OD1 ASP A 8 MN MN A 601 1555 1555 2.16 LINK NE2 HIS A 10 MN MN A 601 1555 1555 2.06 LINK OD1 ASN A 39 MN MN A 601 1555 1555 2.39 LINK OD1 ASN A 39 MN MN A 602 1555 1555 2.38 LINK OD1 ASP A 62 MN MN A 602 1555 1555 2.18 LINK NE2 HIS A 86 MN MN A 602 1555 1555 2.36 LINK ND1 HIS A 115 MN MN A 602 1555 1555 2.26 LINK NE2 HIS A 117 MN MN A 601 1555 1555 2.25 LINK MN MN A 601 O HOH A 603 1555 1555 2.10 LINK MN MN A 602 O HOH A 603 1555 1555 2.09 LINK MN MN A 602 O HOH A 693 1555 1555 2.54 LINK OD1 ASP B 8 MN MN B 701 1555 1555 2.11 LINK NE2 HIS B 10 MN MN B 701 1555 1555 2.19 LINK OD1 ASN B 39 MN MN B 701 1555 1555 2.35 LINK OD1 ASN B 39 MN MN B 702 1555 1555 2.34 LINK OD2 ASP B 62 MN MN B 702 1555 1555 2.07 LINK NE2 HIS B 86 MN MN B 702 1555 1555 2.30 LINK ND1 HIS B 115 MN MN B 702 1555 1555 2.25 LINK NE2 HIS B 117 MN MN B 701 1555 1555 2.32 LINK MN MN B 701 O HOH B 703 1555 1555 2.01 LINK MN MN B 702 O HOH B 703 1555 1555 2.00 LINK MN MN B 702 O HOH B 770 1555 1555 2.42 CISPEP 1 ILE A 11 PRO A 12 0 4.77 CISPEP 2 ILE B 11 PRO B 12 0 10.49 SITE 1 AC1 6 ASP A 8 HIS A 10 ASN A 39 HIS A 117 SITE 2 AC1 6 MN A 602 HOH A 603 SITE 1 AC2 7 ASN A 39 ASP A 62 HIS A 86 HIS A 115 SITE 2 AC2 7 MN A 601 HOH A 603 HOH A 693 SITE 1 AC3 6 ASP B 8 HIS B 10 ASN B 39 HIS B 117 SITE 2 AC3 6 MN B 702 HOH B 703 SITE 1 AC4 7 ASN B 39 ASP B 62 HIS B 86 HIS B 115 SITE 2 AC4 7 MN B 701 HOH B 703 HOH B 770 SITE 1 AC5 7 LYS A 81 ASP A 107 VAL A 108 ASP A 109 SITE 2 AC5 7 LYS A 127 LYS A 181 HOH A 724 SITE 1 AC6 3 ASP A 154 TYR A 163 TYR A 165 SITE 1 AC7 3 ASP B 55 HIS B 57 THR B 76 SITE 1 AC8 4 LEU B 25 VAL B 27 HOH B 829 HOH B 840 SITE 1 AC9 5 PHE A 119 GLU A 120 ALA A 121 PHE A 122 SITE 2 AC9 5 HOH A 698 CRYST1 55.914 68.953 60.519 90.00 106.65 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 0.017885 0.000000 0.005349 0.00000 SCALE2 0.000000 0.014503 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017247 0.00000