HEADER HYDROLASE 19-MAY-17 5VVO
TITLE STRUCTURAL INVESTIGATIONS OF THE SUBSTRATE SPECIFICITY OF HUMAN O-
TITLE 2 GLCNACASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN O-GLCNACASE;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 60-400, 553-704;
COMPND 5 SYNONYM: OGA,BETA-N-ACETYLGLUCOSAMINIDASE,BETA-N-
COMPND 6 ACETYLHEXOSAMINIDASE,BETA-HEXOSAMINIDASE,MENINGIOMA-EXPRESSED ANTIGEN
COMPND 7 5,N-ACETYL-BETA-D-GLUCOSAMINIDASE,N-ACETYL-BETA-GLUCOSAMINIDASE,
COMPND 8 NUCLEAR CYTOPLASMIC O-GLCNACASE AND ACETYLTRANSFERASE,NCOAT;
COMPND 9 EC: 3.2.1.169,3.2.1.-;
COMPND 10 ENGINEERED: YES;
COMPND 11 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: MGEA5, HEXC, KIAA0679, MEA5;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS OGA, HUMAN O-GLCNACASE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR B.LI,J.JIANG,H.LI,C.-W.HU
REVDAT 3 04-OCT-23 5VVO 1 REMARK
REVDAT 2 04-OCT-17 5VVO 1 JRNL
REVDAT 1 27-SEP-17 5VVO 0
JRNL AUTH B.LI,H.LI,C.W.HU,J.JIANG
JRNL TITL STRUCTURAL INSIGHTS INTO THE SUBSTRATE BINDING ADAPTABILITY
JRNL TITL 2 AND SPECIFICITY OF HUMAN O-GLCNACASE.
JRNL REF NAT COMMUN V. 8 666 2017
JRNL REFN ESSN 2041-1723
JRNL PMID 28939839
JRNL DOI 10.1038/S41467-017-00865-1
REMARK 2
REMARK 2 RESOLUTION. 2.60 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0158
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) : 2.60
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 80.57
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1
REMARK 3 NUMBER OF REFLECTIONS : 36678
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) : 0.215
REMARK 3 R VALUE (WORKING SET) : 0.213
REMARK 3 FREE R VALUE : 0.259
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900
REMARK 3 FREE R VALUE TEST SET COUNT : 1878
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) : 2.60
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2484
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.41
REMARK 3 BIN R VALUE (WORKING SET) : 0.3440
REMARK 3 BIN FREE R VALUE SET COUNT : 123
REMARK 3 BIN FREE R VALUE : 0.3800
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 7089
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 132
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 59.10
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.05000
REMARK 3 B22 (A**2) : -0.01000
REMARK 3 B33 (A**2) : -0.03000
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): 0.545
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.305
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.280
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.029
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7277 ; 0.012 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 6654 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9844 ; 1.620 ; 1.951
REMARK 3 BOND ANGLES OTHERS (DEGREES): 15429 ; 1.010 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 858 ; 6.695 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 351 ;33.475 ;23.590
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1259 ;16.973 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;16.549 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1041 ; 0.090 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7985 ; 0.007 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1597 ; 0.002 ; 0.020
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): 3456 ; 4.442 ; 5.780
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3455 ; 4.421 ; 5.779
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4306 ; 6.669 ; 8.662
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4307 ; 6.669 ; 8.663
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3821 ; 4.519 ; 6.175
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3822 ; 4.519 ; 6.176
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5539 ; 7.009 ; 9.080
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8451 ; 9.880 ;66.639
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8437 ; 9.871 ;66.662
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 NCS TYPE: LOCAL
REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1
REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT
REMARK 3 1 A 59 695 B 59 695 26754 0.11 0.05
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 : 1.20
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 5VVO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-MAY-17.
REMARK 100 THE DEPOSITION ID IS D_1000228028.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 31-MAR-17
REMARK 200 TEMPERATURE (KELVIN) : 80
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-F
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.978
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38896
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600
REMARK 200 RESOLUTION RANGE LOW (A) : 80.570
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 6.300
REMARK 200 R MERGE (I) : 0.08400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64
REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3
REMARK 200 DATA REDUNDANCY IN SHELL : 5.70
REMARK 200 R MERGE FOR SHELL (I) : 0.63100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 5TKE
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 55.75
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.024 M AMMONIUM CITRATE TRIBASIC (PH
REMARK 280 7.0), 0.015 M MES MONOHYDRATE, 0.096 M POTASSIUM THIOCYANATE,
REMARK 280 0.25 M SODIUM ACETATE TRIHYDRATE, 0.037 M IMIDAZOLE, 0.002 M
REMARK 280 ZINC SULFATE HEPTAHYDRATE, 9.6 % W/V POLYETHYLENE GLYCOL 3,350,
REMARK 280 2.4 % W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000, AND 4% W/V
REMARK 280 POLYETHYLENE GLYCOL MONOMETHYL ETHER 550, EVAPORATION,
REMARK 280 TEMPERATURE 293K
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 48.41500
REMARK 290 SMTRY3 2 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 7230 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 35090 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 ASN A 335
REMARK 465 MET A 336
REMARK 465 ASN A 337
REMARK 465 GLY A 338
REMARK 465 VAL A 339
REMARK 465 ARG A 340
REMARK 465 LYS A 341
REMARK 465 ASP A 342
REMARK 465 VAL A 343
REMARK 465 VAL A 344
REMARK 465 MET A 345
REMARK 465 THR A 346
REMARK 465 ASP A 347
REMARK 465 SER A 348
REMARK 465 GLU A 349
REMARK 465 ASP A 350
REMARK 465 SER A 351
REMARK 465 THR A 352
REMARK 465 VAL A 353
REMARK 465 SER A 354
REMARK 465 ILE A 355
REMARK 465 GLN A 356
REMARK 465 ILE A 357
REMARK 465 LYS A 358
REMARK 465 LEU A 359
REMARK 465 GLU A 360
REMARK 465 ASN A 361
REMARK 465 GLU A 362
REMARK 465 GLY A 363
REMARK 465 SER A 364
REMARK 465 ASP A 365
REMARK 465 GLU A 366
REMARK 465 ASP A 367
REMARK 465 ILE A 368
REMARK 465 GLU A 369
REMARK 465 THR A 370
REMARK 465 ASP A 371
REMARK 465 VAL A 372
REMARK 465 GLY A 543
REMARK 465 GLY A 544
REMARK 465 GLY A 545
REMARK 465 GLY A 546
REMARK 465 SER A 547
REMARK 465 GLY A 548
REMARK 465 GLY A 549
REMARK 465 GLY A 550
REMARK 465 GLY A 551
REMARK 465 CYS A 663
REMARK 465 ARG A 664
REMARK 465 SER A 665
REMARK 465 HIS A 666
REMARK 465 SER A 667
REMARK 465 SER A 668
REMARK 465 ALA A 669
REMARK 465 GLN A 670
REMARK 465 PHE A 671
REMARK 465 LEU A 672
REMARK 465 ILE A 673
REMARK 465 GLY A 674
REMARK 465 ASP A 675
REMARK 465 GLN A 676
REMARK 465 GLU A 677
REMARK 465 PRO A 678
REMARK 465 TRP A 679
REMARK 465 PHE A 702
REMARK 465 PHE A 703
REMARK 465 GLN A 704
REMARK 465 SER B 334
REMARK 465 ASN B 335
REMARK 465 MET B 336
REMARK 465 ASN B 337
REMARK 465 GLY B 338
REMARK 465 VAL B 339
REMARK 465 ARG B 340
REMARK 465 LYS B 341
REMARK 465 ASP B 342
REMARK 465 VAL B 343
REMARK 465 VAL B 344
REMARK 465 MET B 345
REMARK 465 THR B 346
REMARK 465 ASP B 347
REMARK 465 SER B 348
REMARK 465 GLU B 349
REMARK 465 ASP B 350
REMARK 465 SER B 351
REMARK 465 THR B 352
REMARK 465 VAL B 353
REMARK 465 SER B 354
REMARK 465 ILE B 355
REMARK 465 GLN B 356
REMARK 465 ILE B 357
REMARK 465 LYS B 358
REMARK 465 LEU B 359
REMARK 465 GLU B 360
REMARK 465 ASN B 361
REMARK 465 GLU B 362
REMARK 465 GLY B 363
REMARK 465 SER B 364
REMARK 465 ASP B 365
REMARK 465 GLU B 366
REMARK 465 ASP B 367
REMARK 465 ILE B 368
REMARK 465 GLU B 369
REMARK 465 THR B 370
REMARK 465 ASP B 371
REMARK 465 VAL B 372
REMARK 465 LEU B 373
REMARK 465 VAL B 535
REMARK 465 PRO B 536
REMARK 465 HIS B 537
REMARK 465 GLN B 538
REMARK 465 TYR B 539
REMARK 465 SER B 540
REMARK 465 SER B 541
REMARK 465 ARG B 542
REMARK 465 GLY B 543
REMARK 465 GLY B 544
REMARK 465 GLY B 545
REMARK 465 GLY B 546
REMARK 465 SER B 547
REMARK 465 GLY B 548
REMARK 465 GLY B 549
REMARK 465 GLY B 550
REMARK 465 GLY B 551
REMARK 465 SER B 593
REMARK 465 VAL B 594
REMARK 465 ASN B 595
REMARK 465 CYS B 596
REMARK 465 LYS B 597
REMARK 465 GLY B 598
REMARK 465 LYS B 599
REMARK 465 ASP B 600
REMARK 465 SER B 601
REMARK 465 ASP B 696
REMARK 465 GLY B 697
REMARK 465 ALA B 698
REMARK 465 ASN B 699
REMARK 465 ASP B 700
REMARK 465 LEU B 701
REMARK 465 PHE B 702
REMARK 465 PHE B 703
REMARK 465 GLN B 704
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 SG CYS B 663 NE2 HIS B 666 2.05
REMARK 500 O VAL B 592 O HOH B 801 2.15
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 CYS B 663 CB CYS B 663 SG 0.132
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 ARG B 290 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES
REMARK 500 CYS B 663 CB - CA - C ANGL. DEV. = 11.1 DEGREES
REMARK 500 CYS B 663 CA - CB - SG ANGL. DEV. = 12.1 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 ALA A 96 48.80 -153.26
REMARK 500 ARG A 104 -57.70 -133.59
REMARK 500 ASP A 174 -88.17 -55.29
REMARK 500 ASP A 177 126.64 -28.17
REMARK 500 GLU A 210 -71.00 -47.54
REMARK 500 ASP A 287 114.76 -171.67
REMARK 500 PRO A 314 -163.08 -102.14
REMARK 500 TYR A 566 -88.80 -103.53
REMARK 500 VAL A 594 82.90 -65.16
REMARK 500 LYS A 599 -166.44 -166.78
REMARK 500 ALA B 96 49.47 -154.17
REMARK 500 ARG B 104 -57.89 -135.19
REMARK 500 ASP B 174 -80.41 -61.21
REMARK 500 ALA B 182 158.64 80.05
REMARK 500 ALA B 183 -53.30 70.21
REMARK 500 GLU B 210 -71.23 -46.28
REMARK 500 ASP B 287 111.23 -167.56
REMARK 500 PRO B 314 -163.15 -102.04
REMARK 500 PHE B 391 -159.99 -85.33
REMARK 500 TYR B 566 -89.06 -104.47
REMARK 500 LYS B 603 36.94 -95.38
REMARK 500 ILE B 604 35.42 -96.98
REMARK 500 CYS B 663 9.30 -67.72
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5VVT RELATED DB: PDB
REMARK 900 RELATED ID: 5VVU RELATED DB: PDB
REMARK 900 RELATED ID: 5VVV RELATED DB: PDB
REMARK 900 RELATED ID: 5VVX RELATED DB: PDB
DBREF 5VVO A 60 400 UNP O60502 OGA_HUMAN 60 400
DBREF 5VVO A 553 704 UNP O60502 OGA_HUMAN 553 704
DBREF 5VVO B 60 542 UNP O60502 OGA_HUMAN 60 400
DBREF 5VVO B 553 704 UNP O60502 OGA_HUMAN 553 704
SEQADV 5VVO HIS A 59 UNP O60502 EXPRESSION TAG
SEQADV 5VVO ASN A 175 UNP O60502 ASP 175 ENGINEERED MUTATION
SEQADV 5VVO GLY A 543 UNP O60502 LINKER
SEQADV 5VVO GLY A 544 UNP O60502 LINKER
SEQADV 5VVO GLY A 545 UNP O60502 LINKER
SEQADV 5VVO GLY A 546 UNP O60502 LINKER
SEQADV 5VVO SER A 547 UNP O60502 LINKER
SEQADV 5VVO GLY A 548 UNP O60502 LINKER
SEQADV 5VVO GLY A 549 UNP O60502 LINKER
SEQADV 5VVO GLY A 550 UNP O60502 LINKER
SEQADV 5VVO GLY A 551 UNP O60502 LINKER
SEQADV 5VVO SER A 552 UNP O60502 LINKER
SEQADV 5VVO HIS B 59 UNP O60502 EXPRESSION TAG
SEQADV 5VVO ASN B 175 UNP O60502 ASP 175 ENGINEERED MUTATION
SEQADV 5VVO GLY B 543 UNP O60502 LINKER
SEQADV 5VVO GLY B 544 UNP O60502 LINKER
SEQADV 5VVO GLY B 545 UNP O60502 LINKER
SEQADV 5VVO GLY B 546 UNP O60502 LINKER
SEQADV 5VVO SER B 547 UNP O60502 LINKER
SEQADV 5VVO GLY B 548 UNP O60502 LINKER
SEQADV 5VVO GLY B 549 UNP O60502 LINKER
SEQADV 5VVO GLY B 550 UNP O60502 LINKER
SEQADV 5VVO GLY B 551 UNP O60502 LINKER
SEQADV 5VVO SER B 552 UNP O60502 LINKER
SEQRES 1 A 504 HIS PHE LEU CYS GLY VAL VAL GLU GLY PHE TYR GLY ARG
SEQRES 2 A 504 PRO TRP VAL MET GLU GLN ARG LYS GLU LEU PHE ARG ARG
SEQRES 3 A 504 LEU GLN LYS TRP GLU LEU ASN THR TYR LEU TYR ALA PRO
SEQRES 4 A 504 LYS ASP ASP TYR LYS HIS ARG MET PHE TRP ARG GLU MET
SEQRES 5 A 504 TYR SER VAL GLU GLU ALA GLU GLN LEU MET THR LEU ILE
SEQRES 6 A 504 SER ALA ALA ARG GLU TYR GLU ILE GLU PHE ILE TYR ALA
SEQRES 7 A 504 ILE SER PRO GLY LEU ASP ILE THR PHE SER ASN PRO LYS
SEQRES 8 A 504 GLU VAL SER THR LEU LYS ARG LYS LEU ASP GLN VAL SER
SEQRES 9 A 504 GLN PHE GLY CYS ARG SER PHE ALA LEU LEU PHE ASP ASN
SEQRES 10 A 504 ILE ASP HIS ASN MET CYS ALA ALA ASP LYS GLU VAL PHE
SEQRES 11 A 504 SER SER PHE ALA HIS ALA GLN VAL SER ILE THR ASN GLU
SEQRES 12 A 504 ILE TYR GLN TYR LEU GLY GLU PRO GLU THR PHE LEU PHE
SEQRES 13 A 504 CYS PRO THR GLU TYR CYS GLY THR PHE CYS TYR PRO ASN
SEQRES 14 A 504 VAL SER GLN SER PRO TYR LEU ARG THR VAL GLY GLU LYS
SEQRES 15 A 504 LEU LEU PRO GLY ILE GLU VAL LEU TRP THR GLY PRO LYS
SEQRES 16 A 504 VAL VAL SER LYS GLU ILE PRO VAL GLU SER ILE GLU GLU
SEQRES 17 A 504 VAL SER LYS ILE ILE LYS ARG ALA PRO VAL ILE TRP ASP
SEQRES 18 A 504 ASN ILE HIS ALA ASN ASP TYR ASP GLN LYS ARG LEU PHE
SEQRES 19 A 504 LEU GLY PRO TYR LYS GLY ARG SER THR GLU LEU ILE PRO
SEQRES 20 A 504 ARG LEU LYS GLY VAL LEU THR ASN PRO ASN CYS GLU PHE
SEQRES 21 A 504 GLU ALA ASN TYR VAL ALA ILE HIS THR LEU ALA THR TRP
SEQRES 22 A 504 TYR LYS SER ASN MET ASN GLY VAL ARG LYS ASP VAL VAL
SEQRES 23 A 504 MET THR ASP SER GLU ASP SER THR VAL SER ILE GLN ILE
SEQRES 24 A 504 LYS LEU GLU ASN GLU GLY SER ASP GLU ASP ILE GLU THR
SEQRES 25 A 504 ASP VAL LEU TYR SER PRO GLN MET ALA LEU LYS LEU ALA
SEQRES 26 A 504 LEU THR GLU TRP LEU GLN GLU PHE GLY VAL PRO HIS GLN
SEQRES 27 A 504 TYR SER SER ARG GLY GLY GLY GLY SER GLY GLY GLY GLY
SEQRES 28 A 504 SER VAL THR LEU GLU ASP LEU GLN LEU LEU ALA ASP LEU
SEQRES 29 A 504 PHE TYR LEU PRO TYR GLU HIS GLY PRO LYS GLY ALA GLN
SEQRES 30 A 504 MET LEU ARG GLU PHE GLN TRP LEU ARG ALA ASN SER SER
SEQRES 31 A 504 VAL VAL SER VAL ASN CYS LYS GLY LYS ASP SER GLU LYS
SEQRES 32 A 504 ILE GLU GLU TRP ARG SER ARG ALA ALA LYS PHE GLU GLU
SEQRES 33 A 504 MET CYS GLY LEU VAL MET GLY MET PHE THR ARG LEU SER
SEQRES 34 A 504 ASN CYS ALA ASN ARG THR ILE LEU TYR ASP MET TYR SER
SEQRES 35 A 504 TYR VAL TRP ASP ILE LYS SER ILE MET SER MET VAL LYS
SEQRES 36 A 504 SER PHE VAL GLN TRP LEU GLY CYS ARG SER HIS SER SER
SEQRES 37 A 504 ALA GLN PHE LEU ILE GLY ASP GLN GLU PRO TRP ALA PHE
SEQRES 38 A 504 ARG GLY GLY LEU ALA GLY GLU PHE GLN ARG LEU LEU PRO
SEQRES 39 A 504 ILE ASP GLY ALA ASN ASP LEU PHE PHE GLN
SEQRES 1 B 504 HIS PHE LEU CYS GLY VAL VAL GLU GLY PHE TYR GLY ARG
SEQRES 2 B 504 PRO TRP VAL MET GLU GLN ARG LYS GLU LEU PHE ARG ARG
SEQRES 3 B 504 LEU GLN LYS TRP GLU LEU ASN THR TYR LEU TYR ALA PRO
SEQRES 4 B 504 LYS ASP ASP TYR LYS HIS ARG MET PHE TRP ARG GLU MET
SEQRES 5 B 504 TYR SER VAL GLU GLU ALA GLU GLN LEU MET THR LEU ILE
SEQRES 6 B 504 SER ALA ALA ARG GLU TYR GLU ILE GLU PHE ILE TYR ALA
SEQRES 7 B 504 ILE SER PRO GLY LEU ASP ILE THR PHE SER ASN PRO LYS
SEQRES 8 B 504 GLU VAL SER THR LEU LYS ARG LYS LEU ASP GLN VAL SER
SEQRES 9 B 504 GLN PHE GLY CYS ARG SER PHE ALA LEU LEU PHE ASP ASN
SEQRES 10 B 504 ILE ASP HIS ASN MET CYS ALA ALA ASP LYS GLU VAL PHE
SEQRES 11 B 504 SER SER PHE ALA HIS ALA GLN VAL SER ILE THR ASN GLU
SEQRES 12 B 504 ILE TYR GLN TYR LEU GLY GLU PRO GLU THR PHE LEU PHE
SEQRES 13 B 504 CYS PRO THR GLU TYR CYS GLY THR PHE CYS TYR PRO ASN
SEQRES 14 B 504 VAL SER GLN SER PRO TYR LEU ARG THR VAL GLY GLU LYS
SEQRES 15 B 504 LEU LEU PRO GLY ILE GLU VAL LEU TRP THR GLY PRO LYS
SEQRES 16 B 504 VAL VAL SER LYS GLU ILE PRO VAL GLU SER ILE GLU GLU
SEQRES 17 B 504 VAL SER LYS ILE ILE LYS ARG ALA PRO VAL ILE TRP ASP
SEQRES 18 B 504 ASN ILE HIS ALA ASN ASP TYR ASP GLN LYS ARG LEU PHE
SEQRES 19 B 504 LEU GLY PRO TYR LYS GLY ARG SER THR GLU LEU ILE PRO
SEQRES 20 B 504 ARG LEU LYS GLY VAL LEU THR ASN PRO ASN CYS GLU PHE
SEQRES 21 B 504 GLU ALA ASN TYR VAL ALA ILE HIS THR LEU ALA THR TRP
SEQRES 22 B 504 TYR LYS SER ASN MET ASN GLY VAL ARG LYS ASP VAL VAL
SEQRES 23 B 504 MET THR ASP SER GLU ASP SER THR VAL SER ILE GLN ILE
SEQRES 24 B 504 LYS LEU GLU ASN GLU GLY SER ASP GLU ASP ILE GLU THR
SEQRES 25 B 504 ASP VAL LEU TYR SER PRO GLN MET ALA LEU LYS LEU ALA
SEQRES 26 B 504 LEU THR GLU TRP LEU GLN GLU PHE GLY VAL PRO HIS GLN
SEQRES 27 B 504 TYR SER SER ARG GLY GLY GLY GLY SER GLY GLY GLY GLY
SEQRES 28 B 504 SER VAL THR LEU GLU ASP LEU GLN LEU LEU ALA ASP LEU
SEQRES 29 B 504 PHE TYR LEU PRO TYR GLU HIS GLY PRO LYS GLY ALA GLN
SEQRES 30 B 504 MET LEU ARG GLU PHE GLN TRP LEU ARG ALA ASN SER SER
SEQRES 31 B 504 VAL VAL SER VAL ASN CYS LYS GLY LYS ASP SER GLU LYS
SEQRES 32 B 504 ILE GLU GLU TRP ARG SER ARG ALA ALA LYS PHE GLU GLU
SEQRES 33 B 504 MET CYS GLY LEU VAL MET GLY MET PHE THR ARG LEU SER
SEQRES 34 B 504 ASN CYS ALA ASN ARG THR ILE LEU TYR ASP MET TYR SER
SEQRES 35 B 504 TYR VAL TRP ASP ILE LYS SER ILE MET SER MET VAL LYS
SEQRES 36 B 504 SER PHE VAL GLN TRP LEU GLY CYS ARG SER HIS SER SER
SEQRES 37 B 504 ALA GLN PHE LEU ILE GLY ASP GLN GLU PRO TRP ALA PHE
SEQRES 38 B 504 ARG GLY GLY LEU ALA GLY GLU PHE GLN ARG LEU LEU PRO
SEQRES 39 B 504 ILE ASP GLY ALA ASN ASP LEU PHE PHE GLN
FORMUL 3 HOH *132(H2 O)
HELIX 1 AA1 VAL A 74 TRP A 88 1 15
HELIX 2 AA2 SER A 112 TYR A 129 1 18
HELIX 3 AA3 ASN A 147 GLN A 163 1 17
HELIX 4 AA4 CYS A 181 PHE A 188 1 8
HELIX 5 AA5 SER A 190 LEU A 206 1 17
HELIX 6 AA6 CYS A 220 CYS A 224 5 5
HELIX 7 AA7 SER A 231 LEU A 241 1 11
HELIX 8 AA8 PRO A 260 LYS A 272 1 13
HELIX 9 AA9 SER A 300 LEU A 307 5 8
HELIX 10 AB1 GLU A 317 ALA A 320 5 4
HELIX 11 AB2 ASN A 321 SER A 334 1 14
HELIX 12 AB3 SER A 375 LEU A 388 1 14
HELIX 13 AB4 GLN A 389 PHE A 391 5 3
HELIX 14 AB5 THR A 554 PHE A 565 1 12
HELIX 15 AB6 GLY A 572 ASN A 588 1 17
HELIX 16 AB7 ASP A 600 ASN A 630 1 31
HELIX 17 AB8 ASN A 633 GLY A 662 1 30
HELIX 18 AB9 GLY A 683 LEU A 693 1 11
HELIX 19 AC1 VAL B 74 TRP B 88 1 15
HELIX 20 AC2 SER B 112 TYR B 129 1 18
HELIX 21 AC3 ASN B 147 GLN B 163 1 17
HELIX 22 AC4 ALA B 183 PHE B 188 1 6
HELIX 23 AC5 SER B 190 LEU B 206 1 17
HELIX 24 AC6 CYS B 220 CYS B 224 5 5
HELIX 25 AC7 SER B 231 LEU B 241 1 11
HELIX 26 AC8 PRO B 260 LYS B 272 1 13
HELIX 27 AC9 GLU B 302 LEU B 307 1 6
HELIX 28 AD1 GLU B 317 ALA B 320 5 4
HELIX 29 AD2 ASN B 321 LYS B 333 1 13
HELIX 30 AD3 SER B 375 GLU B 390 1 16
HELIX 31 AD4 THR B 554 PHE B 565 1 12
HELIX 32 AD5 GLY B 572 ASN B 588 1 17
HELIX 33 AD6 SER B 589 VAL B 592 5 4
HELIX 34 AD7 ILE B 604 ASN B 630 1 27
HELIX 35 AD8 ASN B 633 CYS B 663 1 31
HELIX 36 AD9 ARG B 664 HIS B 666 5 3
HELIX 37 AE1 GLU B 677 PHE B 681 5 5
HELIX 38 AE2 GLY B 683 LEU B 693 1 11
SHEET 1 AA1 9 LEU A 61 GLU A 66 0
SHEET 2 AA1 9 THR A 92 TYR A 95 1 O LEU A 94 N GLU A 66
SHEET 3 AA1 9 GLU A 132 ILE A 137 1 O ILE A 134 N TYR A 95
SHEET 4 AA1 9 SER A 168 LEU A 172 1 O LEU A 172 N ILE A 137
SHEET 5 AA1 9 PHE A 212 CYS A 215 1 O LEU A 213 N LEU A 171
SHEET 6 AA1 9 GLU A 246 TRP A 249 1 O GLU A 246 N PHE A 212
SHEET 7 AA1 9 VAL A 276 ASP A 279 1 O VAL A 276 N VAL A 247
SHEET 8 AA1 9 GLY A 309 THR A 312 1 O LEU A 311 N ILE A 277
SHEET 9 AA1 9 LEU A 61 GLU A 66 1 N LEU A 61 O VAL A 310
SHEET 1 AA2 9 LEU B 61 GLU B 66 0
SHEET 2 AA2 9 THR B 92 TYR B 95 1 O LEU B 94 N GLU B 66
SHEET 3 AA2 9 GLU B 132 ILE B 137 1 O ILE B 134 N TYR B 95
SHEET 4 AA2 9 SER B 168 LEU B 172 1 O LEU B 172 N ILE B 137
SHEET 5 AA2 9 PHE B 212 CYS B 215 1 O LEU B 213 N LEU B 171
SHEET 6 AA2 9 GLU B 246 TRP B 249 1 O GLU B 246 N PHE B 212
SHEET 7 AA2 9 VAL B 276 ASP B 279 1 O VAL B 276 N VAL B 247
SHEET 8 AA2 9 GLY B 309 THR B 312 1 O LEU B 311 N ILE B 277
SHEET 9 AA2 9 LEU B 61 GLU B 66 1 N LEU B 61 O VAL B 310
CISPEP 1 TYR A 225 PRO A 226 0 -10.86
CISPEP 2 TYR B 225 PRO B 226 0 -11.33
CRYST1 82.404 96.830 89.075 90.00 115.24 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 0.012135 0.000000 0.005720 0.00000
SCALE2 0.000000 0.010327 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012411 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
